Appendix A — Microbe Set Enrichment Analysis (MSEA)
Similar to gene set enrichment analyses for genes (Subramanian et al. 2005), an obvious next step following differential abundance analysis in microbiome studies is to conduct enrichment analysis for microbe sets, known as microbe set enrichment analysis (MSEA) (Kou et al. 2020). Similar to GSEA, the primary goal of MSEA is to detect the modest but coordinated changes in pre-specified sets of related microbial features. Such a set might include all the microbes in a specific pathway or microbial genes that have been shown to be co-regulated based on previously published studies. Like GSEA, MSEA aggregates the per-feature statistics across microbes within a microbe set. This corresponds to the hypothesis that many relevant phenotype differences are manifested by small but consistent changes in a set of features.
Subramanian, Aravind, Pablo Tamayo, Vamsi K Mootha, Sayan Mukherjee, Benjamin L Ebert, Michael A Gillette, Amanda Paulovich, et al. 2005. “Gene Set Enrichment Analysis: A Knowledge-Based Approach for Interpreting Genome-Wide Expression Profiles.” Proceedings of the National Academy of Sciences 102 (43): 15545–50. https://doi.org/10.1073/pnas.0506580102.
Kou, Yan, Xiaomin Xu, Zhengnong Zhu, Lei Dai, and Yan Tan. 2020. “Microbe-Set Enrichment Analysis Facilitates Functional Interpretation of Microbiome Profiling Data.” Scientific Reports 10 (1): 21466. https://doi.org/10.1038/s41598-020-78511-y.
The goal of the MSEA approach is to determine if the members of S (microbe set) are randomly distributed throughout the ranked list of features (L) or primarily found at the top or bottom. We will use the R package gsEasy to conduct the MSEA test described by Subramanian et al. (2005).
A.1 Input data for MSEA using species relative abundance data
In this chapter, we will use the publicly available Inflammatory Bowel Diseases (IBD) microbiome data from the integrative Human Microbiome Project (iHMP) available from the curatedMetagenomicData package (Lloyd-Price et al. 2019). We aim to conduct MSEA analysis based on both taxonomic profiles (species relative abundances) and functional profiles (pathway relative abundances).
Lloyd-Price, Jason, Cesar Arze, Ashwin N. Ananthakrishnan, Melanie Schirmer, Julian Avila-Pacheco, Tiffany W. Poon, Elizabeth Andrews, et al. 2019. “Multi-Omics of the Gut Microbial Ecosystem in Inflammatory Bowel Diseases.” Nature 569 (7758): 655–62. https://doi.org/https://doi.org/10.1038/s41586-019-1237-9.
A.2 Performing the MSEA analysis with species relative abundance data
We will first prepare the input feature table and sample metadata for differential abundance analysis using MaAsLin2 (Mallick et al. 2021). The ranked feature list from the differential abundance analysis serves as an input for the MSEA.
Mallick, Himel, Ali Rahnavard, Lauren J. McIver, Siyuan Ma, Yancong Zhang, Long H. Nguyen, Timothy L. Tickle, et al. 2021. “Multivariable Association Discovery in Population-Scale Meta-Omics Studies.” PLOS Computational Biology 17 (11): e1009442. https://doi.org/https://doi.org/10.1371/journal.pcbi.1009442.
##################
# Load iHMP data #
##################
library(curatedMetagenomicData)
library(dplyr)
se_relative <- sampleMetadata |>
filter(study_name == "HMP_2019_ibdmdb") |>
returnSamples("relative_abundance", rownames = "short")
##########################
# Create sample metadata #
##########################
sample_metadata <-
colData(se_relative) |>
as.data.frame() |> filter(visit_number == 1) |>
dplyr::select(c("age", "disease", "antibiotics_current_use"))
#################
# Set reference #
#################
sample_metadata$disease <- as.factor(sample_metadata$disease)
sample_metadata$disease <- relevel(sample_metadata$disease, 'healthy')
###########################
# Create species features #
###########################
feature_species_t <- as.data.frame(assay(se_relative))
rownames(feature_species_t) <- sub('.*s__', '', rownames(feature_species_t))
##############################
# Subset to baseline samples #
##############################
feature_species <- as.data.frame(t(feature_species_t))
feature_species <- feature_species[rownames(sample_metadata),]
feature_species <- feature_species / 100
rm(feature_species_t); rm(se_relative)In the next step, we will use MaAsLin2 to fit a multivariable regression model for testing the association between microbial species abundance versus IBD diagnosis. The analysis method we use here is “LM”, which is the default setting. We also adjust for age and antibiotic usage, following the original study.
library(Maaslin2)
fit_data = Maaslin2(
input_data = feature_species,
input_metadata = sample_metadata,
normalization = "NONE",
output = "output_species",
fixed_effects = c("disease", "age", "antibiotics_current_use"))
## [1] "Creating output folder"
## [1] "Creating output feature tables folder"
## [1] "Creating output fits folder"
## [1] "Creating output figures folder"
## 2025-03-22 22:11:26.826159 INFO::Writing function arguments to log file
## 2025-03-22 22:11:26.841385 INFO::Verifying options selected are valid
## 2025-03-22 22:11:26.872998 INFO::Determining format of input files
## 2025-03-22 22:11:26.873656 INFO::Input format is data samples as rows and metadata samples as rows
## 2025-03-22 22:11:26.879923 INFO::Formula for fixed effects: expr ~ disease + age + antibiotics_current_use
## 2025-03-22 22:11:26.880663 INFO::Factor detected for categorial metadata 'disease'. Provide a reference argument or manually set factor ordering to change reference level.
## 2025-03-22 22:11:26.881304 INFO::Filter data based on min abundance and min prevalence
## 2025-03-22 22:11:26.881775 INFO::Total samples in data: 136
## 2025-03-22 22:11:26.882202 INFO::Min samples required with min abundance for a feature not to be filtered: 13.600000
## 2025-03-22 22:11:26.888399 INFO::Total filtered features: 458
## 2025-03-22 22:11:26.889189 INFO::Filtered feature names from abundance and prevalence filtering: species.Clostridiales.bacterium.1_7_47FAA, species.Enterocloster.asparagiformis, species.Gordonibacter.pamelaeae, species.Firmicutes.bacterium.CAG.424, species.Adlercreutzia.equolifaciens, species.Adlercreutzia.equolifaciens_1, species.Anaerotruncus.sp..CAG.528, species.Parabacteroides.johnsonii, species.Erysipelothrix.larvae, species.Proteus.mirabilis, species.Bacteroides.sp..43_108, species.Blautia.producta, species.Tyzzerella.nexilis, species.Ruminococcus.obeum.CAG.39, species..Clostridium..scindens, species.Blautia.hydrogenotrophica, species.Lachnoclostridium.sp..An181, species.Candidatus.Stoquefichus.sp..KLE1796, species.Gemmiger.sp..An87, species.Lachnoclostridium.sp..An138, species.Harryflintia.acetispora, species.Streptococcus.thermophilus, species.Prevotella.buccae, species.Dorea.sp..CAG.317, species.Proteus.vulgaris, species.Proteus.hauseri, species..Clostridium..spiroforme, species.Blautia.hansenii, species.Eubacterium.sp..OM08.24, species.Parabacteroides.sp..CAG.409, species.Desulfovibrio.piger, species.Clostridium.sp..CAG.242, species.Pseudoflavonifractor.sp..An184, species.Clostridiales.bacterium.CHKCI006, species.Pseudoflavonifractor.sp..An85, species.Christensenella.minuta, species.Bifidobacterium.catenulatum, species.Slackia.isoflavoniconvertens, species.Alistipes.inops, species.Haemophilus.pittmaniae, species.Amedibacillus.dolichus, species.Eubacterium.dolichum.CAG.375, species.Turicibacter.sanguinis, species.Lactobacillus.delbrueckii, species.Aeriscardovia.aeriphila, species.Firmicutes.bacterium.CAG.145, species.Klebsiella.quasipneumoniae, genus.Enterobacter, species.Cutibacterium.granulosum, genus.Pseudomonas, species.Methanobrevibacter.smithii, species.Porphyromonas.asaccharolytica, species.Clostridium.perfringens, species.Clostridium.paraputrificum, species.Limosilactobacillus.fermentum, species.Prevotella.sp..CAG.279, species.Fusobacterium.ulcerans, species.Bifidobacterium.breve, species.Prevotella.sp..CAG.891, species.Lactococcus.piscium, species.Klebsiella.oxytoca, species.Citrobacter.freundii, species.Citrobacter.braakii, species.Bifidobacterium.animalis, species.Citrobacter.youngae, species.Lactobacillus.acidophilus, species.Anaeroglobus.geminatus, species.Bifidobacterium.dentium, species.Clostridium.neonatale, species.Clostridioides.difficile, species.Enterococcus.faecium, species.Morganella.morganii, species.Streptococcus.oralis, species.Klebsiella.michiganensis, species.Clostridium.sp..chh4.2, species.Bacteroides.nordii, species.Klebsiella.aerogenes, species.Leclercia.adecarboxylata, species.Enterobacter.mori, species.Kluyvera.ascorbata, species.Pseudoflavonifractor.capillosus, species.Ruminococcaceae.bacterium.D5, species.Raoultella.planticola, species.Roseburia.sp..CAG.303, species.Alloscardovia.omnicolens, species.Eubacterium.sp..CAG.180, species.Eubacterium.sp..CAG.274, species.Cutibacterium.acnes, species.Dialister.sp..CAG.357, species.Bacteroides.oleiciplenus, species.Coprobacter.secundus, species.Kocuria.palustris, species.Acinetobacter.lwoffii, species.Micrococcus.lylae, species.Pararheinheimera.mesophila, species.Desulfovibrionaceae.bacterium, species.Massilimicrobiota.timonensis, species.Fretibacterium.fastidiosum, species.Streptococcus.vestibularis, species.Clostridium.sp..CAG.411, species.Megamonas.funiformis, species.Megamonas.hypermegale, species.Megamonas.funiformis.CAG.377, species.Streptococcus.gordonii, species.Coprobacillus.cateniformis, species.Prevotella.colorans, species.Prevotella.buccalis, species.Anaerofustis.stercorihominis, species.Latilactobacillus.sakei, species.Clostridium.disporicum, species.Ruminococcus.sp..CAG.330, species.Streptococcus.agalactiae, species.Aggregatibacter.segnis, species.Fusobacterium.nucleatum, species.Bifidobacterium.pseudolongum, species.Allisonella.histaminiformans, species.Prevotella.bivia, species.Clostridium.sp..CAG.590, species.Ruminococcus.callidus, species.Holdemanella.biformis, species.Escherichia.marmotae, species.Terrisporobacter.othiniensis, species.Porphyromonas.somerae, species.Prevotella.salivae, species.Citrobacter.amalonaticus, species.Ligilactobacillus.salivarius, species.Megasphaera.micronuciformis, species.Neisseria.sp..oral.taxon.014, species.Anaerostipes.caccae, species.Blautia.argi, species.Escherichia.albertii, species.Prevotella.disiens, species.Porphyromonas.uenonis, species.Peptococcus.niger, species.Bacteroides.sp..CAG.144, species.Eubacterium.sp..An11, species.Blautia.coccoides, species.Oxalobacter.formigenes, species.Tractidigestivibacter.scatoligenes, species.Dialister.pneumosintes, species.Megasphaera.sp..DISK.18, species.Clostridium.sp..CAG.167, species.Hafnia.paralvei, species.Alistipes.onderdonkii, species.Coprobacter.sp., species.Corynebacterium.matruchotii, species.Bacteroides.stercorirosoris, species.Staphylococcus.epidermidis, species.Parabacteroides.goldsteinii, species.Roseburia.sp..CAG.182, species.Oscillibacter.sp..PC13, species.Firmicutes.bacterium.CAG.110, species.Prevotella.sp..885, species.Parvimonas.micra, species.Peptostreptococcus.stomatis, species.Moraxella.osloensis, species.Enhydrobacter.aerosaccus, species.Micrococcus.luteus, species.Micrococcus.aloeverae, genus.Streptococcus, species.Dialister.micraerophilus, species.Campylobacter.concisus, species.Megasphaera.sp..MJR8396C, species.Cloacibacillus.porcorum, species.Desulfovibrio.fairfieldensis, species.Phascolarctobacterium.sp..CAG.266, species.Rikenella.microfusus, species.Roseburia.sp..CAG.309, species.Flavonifractor.sp..An10, species.Victivallis.vadensis, species.Firmicutes.bacterium.CAG.95, species.Enorma.massiliensis, species.Citrobacter.pasteurii, species.Streptococcus.salivarius.CAG.79, species.Veillonella.seminalis, species.Enterococcus.faecalis, species.Streptococcus.mitis, species.Butyricicoccus.pullicaecorum, species.Prevotella.corporis, species.Lachnoclostridium.sp..An131, species.Lachnoclostridium.sp..An118, species..Clostridium..methylpentosum, species.Haemophilus.parahaemolyticus, species.Neisseria.flavescens, species.Veillonella.rogosae, species.Neisseria.subflava, species.Sharpea.azabuensis, species.Anaerofilum.sp..An201, species.Romboutsia.ilealis, species.Fusobacterium.periodonticum, species.Lachnoclostridium.sp..An14, species.Flavonifractor.sp..An100, species.Clostridium.sp..CAG.253, species.Arthrospira.platensis, species.Lactobacillus.amylovorus, species.Limosilactobacillus.oris, species.Streptococcus.lutetiensis, species.Weissella.cibaria, species.Rothia.mucilaginosa, species.Streptococcus.pasteurianus, species.Prevotella.melaninogenica, species.Prevotella.jejuni, species.Veillonella.tobetsuensis, species.Streptococcus.sp..M334, species.Actinomyces.sp..ICM47, species.Streptococcus.sp..A12, species.Clostridium.sp..CAG.678, species.Candidatus.Methanomassiliicoccus.intestinalis, species.Candidatus.Gastranaerophilales.bacterium, species.Prevotella.denticola, species.Leuconostoc.lactis, species.Prevotella.oris, species.Prevotella.dentalis, species..Eubacterium..infirmum, species.Shuttleworthia.satelles, species.Prevotella.nigrescens, species.Enterococcus.hirae, species.Adlercreutzia.caecimuris, species.Citrobacter.portucalensis, species.Raoultella.ornithinolytica, species.Dysgonomonas.mossii, species.Firmicutes.bacterium.CAG.646, species.Streptococcus.gallolyticus, species.Christensenella.hongkongensis, species.Lactobacillus.paragasseri, species.Lactobacillus.gasseri, species.Peptostreptococcus.anaerobius, species.Acinetobacter.ursingii, species.Lactococcus.lactis, species.Odoribacter.laneus, species.Haemophilus.sputorum, species.Peptoniphilus.harei, species.Pediococcus.acidilactici, species.Fusobacterium.gonidiaformans, species.Fusobacterium.equinum, species.Leuconostoc.garlicum, species.Campylobacter.showae, species.Aeromonas.hydrophila, species.Aeromonas.dhakensis, species.Prevotella.stercorea, species.Phascolarctobacterium.succinatutens, species.Prevotella.sp..AM42.24, species.Blastocystis.sp..subtype.1, species.Bifidobacterium.angulatum, species.Prevotella.timonensis, species.Butyrivibrio.crossotus, species.Limosilactobacillus.vaginalis, species.Ligilactobacillus.ruminis, species.Weissella.confusa, species.Streptococcus.mutans, species.Clostridium.celatum, species.Streptococcus.australis, species.Streptococcus.sanguinis, species.Schaalia.turicensis, species.Peptoniphilus.duerdenii, species.Clostridium.baratii, species.Streptococcus.sp..F0442, species.Prevotella.sp..CAG.520, species.Cronobacter.sakazakii, species.Actinomyces.urogenitalis, species.Actinomyces.graevenitzii, species.Parvimonas.sp..oral.taxon.110, species.Eikenella.corrodens, species.Parvimonas.sp..oral.taxon.393, species.Anaerococcus.vaginalis, species.Gemella.asaccharolytica, species.Lachnospiraceae.bacterium.2_1_46FAA, species.Veillonella.sp..CAG.933, species.Lacticaseibacillus.rhamnosus, species.Campylobacter.upsaliensis, species.Lachnospiraceae.bacterium.oral.taxon.096, species.Campylobacter.gracilis, species.Gemmiger.sp..An50, species.Scardovia.wiggsiae, species.Limosilactobacillus.reuteri, species.Enterococcus.avium, species.Enterococcus.thailandicus, species.Paucilactobacillus.vaccinostercus, species.Enterococcus.casseliflavus, species.Bifidobacterium.pullorum, species.Actinomyces.sp..oral.taxon.180, species.Enterococcus.sp..3H8_DIV0648, species.Enterococcus.gallinarum, species.Bifidobacterium.pullorum_1, species.Bifidobacterium.pullorum_2, species.Varibaculum.cambriense, species.Veillonella.rodentium, species.Lactobacillus.crispatus, species.Lawsonella.clevelandensis, species.Porphyromonas.sp..HMSC065F10, species.Citrobacter.werkmanii, species.Lactobacillus.johnsonii, species.Sarcina.ventriculi, species.Streptococcus.macedonicus, species.Klebsiella.variicola.CAG.634, species.Phytobacter.palmae, species.Enterococcus.raffinosus, species.Prevotella.amnii, species.Catenibacterium.mitsuokai, species.Saccharomyces.cerevisiae, species.Eubacterium.limosum, species.Staphylococcus.hominis, species.Alloprevotella.tannerae, species.Haemophilus.paraphrohaemolyticus, species..Eubacterium..brachy, species.Ruminococcus.sp..CAG.403, species.Fannyhessea.vaginae, species.Cronobacter.malonaticus, species.Streptococcus.infantis, species.Actinomyces.sp..oral.taxon.181, species.Clostridium.butyricum, species.Abiotrophia.sp..HMSC24B09, species.Gemella.haemolysans, species.Firmicutes.bacterium.CAG.170, species.Solobacterium.moorei, species.Pseudomonas.guguanensis, species.Lactobacillus.jensenii, species.Clostridium.cadaveris, species.Aggregatibacter.sp..oral.taxon.458, species.Anaerocolumna.aminovalerica, species.Clostridium.sporogenes, species.Clostridium.botulinum, species.Campylobacter.hominis, species.Murimonas.intestini, species.Clostridium.sp..CAG.964, species.Pediococcus.pentosaceus, species.Corynebacterium.amycolatum, species.Parvimonas.sp..KA00067, species.Bacteroidales.bacterium.KA00251, species.Fusobacterium.mortiferum, species.Lacrimispora.celerecrescens, species.Butyrivibrio.sp..CAG.318, species.Cellulosilyticum.lentocellum, species.Eubacteriaceae.bacterium.CHKCI005, species.Eubacterium.coprostanoligenes, species.Firmicutes.bacterium.CAG.238, species.Dysgonomonas.gadei, species.Bacteroides.fluxus, species.Bacteroides.sp..D2, species.Citrobacter.farmeri, species.Gemella.sanguinis, species.Sanguibacteroides.justesenii, species.Porphyromonas.endodontalis, species.Streptococcus.peroris, species.Actinomyces.sp..HPA0247, species.Lactiplantibacillus.plantarum, species.Limosilactobacillus.mucosae, species.Providencia.alcalifaciens, species.Robinsoniella.sp..RHS, species.Fructilactobacillus.sanfranciscensis, species.Prevotella.sp..CAG.1185, species.Peptoniphilus.lacrimalis, species.Gemella.morbillorum, species.Frigoribacterium.sp..Leaf8, species.Clostridium.sp..MSTE9, species..Clostridium..hylemonae, species.Treponema.lecithinolyticum, species.Faecalicoccus.pleomorphus, species.Flavonifractor.sp..An306, species.Prevotella.oralis, species.Peptoniphilus.sp..BV3C26, species.Brachyspira.pilosicoli, species.Bacteroides.sp..OM08.11, species.Proteus.penneri, species.Corynebacterium.kroppenstedtii, species.Faecalitalea.cylindroides, species.Wohlfahrtiimonas.chitiniclastica, species.Bacteroides.clarus, species.Acidaminococcus.sp..CAG.542, species.Peptoniphilus.coxii, species.Alistipes.timonensis, species.Clostridium.sp..D5, species.Prevotella.bergensis, species.Ruminococcus.sp..CAG.563, species.Kluyvera.cryocrescens, species.Ezakiella.coagulans, species..Bacteroides..pectinophilus, species.Bacteroides.sp..CAG.661, species.Bacteroides.sp..CAG.598, species.Comamonas.kerstersii, species.Firmicutes.bacterium.CAG.534, species.Clostridium.sp..CAG.413, species.Schaalia.odontolytica, species.Streptococcus.cristatus, species.Actinomyces.sp..HMSC035G02, species.Lancefieldella.rimae, species.Streptococcus.milleri, species.Finegoldia.magna, species.Lancefieldella.parvula, species.Prevotella.oulorum, species.Dellaglioa.algida, species.Lactonifactor.longoviformis, species.Hafnia.alvei, species.Neisseria.cinerea, species.Corynebacterium.oculi, species.Ruminococcus.sp..CAG.488, species.Corynebacterium.accolens, species.Prevotella.sp..S7.1.8, species.Campylobacter.ureolyticus, species.Atopobium.deltae, species.Gleimia.europaea, species.Mitsuokella.jalaludinii, species.Mitsuokella.multacida, species.Peptoniphilus.sp..HMSC062D09, species.Anaerococcus.lactolyticus, species.Granulicatella.adiacens, species.Anaerosporobacter.mobilis, species.Clostridium.sp..7_2_43FAA, species.Kosakonia.sacchari, species.Staphylococcus.aureus, species.Ligilactobacillus.animalis, species.Weissella.viridescens, species.Dysgonomonas.sp..37.18, species.Serratia.liquefaciens, species.Streptococcus.sp..HPH0090, species.Anaerostipes.sp..494a, species.Lactococcus.petauri, species.Obesumbacterium.proteus, species.Fusobacterium.sp..oral.taxon.370, species..Butyribacterium..methylotrophicum, species.Phocaeicola.sartorii, species.Bacteroides.sp..CAG.530, species.Megasphaera.elsdenii, species.Prevotella.sp..CAG.1092, species.Fusobacterium.sp..CAG.439, species.Anaeromassilibacillus.sp..An172, species.Aggregatibacter.aphrophilus, species.Aerococcus.urinaeequi, species.Pseudomonas.fragi, species.Thermoleophilum.album, species.Bacteroides.sp..CAG.633, species.Serratia.marcescens, species.Actinotignum.timonense, species.Fusobacterium.naviforme, species.Haemophilus.influenzae, species.Prevotella.intermedia, species.Bacteroidetes.oral.taxon.274, species.Citrobacter.europaeus, species.Bifidobacterium.asteroides, species.Enterococcus.durans, species.Enterococcus.pseudoavium, species.Microvirgula.aerodenitrificans, species.Yersinia.frederiksenii, species.Faecalicatena.orotica, species.Enterococcus.asini, species.Paenibacillus.macerans, species.Bavariicoccus.seileri, species.Kluyvera.georgiana, species.Prevotella.histicola, species.Prevotella.pallens, species.Chlamydia.ibidis, species.Enterococcus.mundtii, species.Anaerostipes.sp..992a, species.Actinobaculum.sp..oral.taxon.183, species.Lachnoclostridium.sp..An298, species.Haemophilus.haemolyticus, species.Enterococcus.dispar, species.Atopobium.minutum
## 2025-03-22 22:11:26.892815 INFO::Total filtered features with variance filtering: 0
## 2025-03-22 22:11:26.893332 INFO::Filtered feature names from variance filtering:
## 2025-03-22 22:11:26.893796 INFO::Running selected normalization method: NONE
## 2025-03-22 22:11:26.894269 INFO::Applying z-score to standardize continuous metadata
## 2025-03-22 22:11:26.898519 INFO::Running selected transform method: LOG
## 2025-03-22 22:11:26.901394 INFO::Running selected analysis method: LM
## 2025-03-22 22:11:26.904963 INFO::Fitting model to feature number 1, species.Phocaeicola.vulgatus
## 2025-03-22 22:11:26.911034 INFO::Fitting model to feature number 2, species.Bacteroides.uniformis
## 2025-03-22 22:11:26.914294 INFO::Fitting model to feature number 3, species.Bacteroides.thetaiotaomicron
## 2025-03-22 22:11:26.916713 INFO::Fitting model to feature number 4, species.Faecalibacterium.prausnitzii
## 2025-03-22 22:11:26.919037 INFO::Fitting model to feature number 5, species.Roseburia.faecis
## 2025-03-22 22:11:26.921315 INFO::Fitting model to feature number 6, species.Bacteroides.caccae
## 2025-03-22 22:11:26.923644 INFO::Fitting model to feature number 7, species.Enterocloster.clostridioformis
## 2025-03-22 22:11:26.925937 INFO::Fitting model to feature number 8, species.Bacteroides.fragilis
## 2025-03-22 22:11:26.928295 INFO::Fitting model to feature number 9, species.Fusicatenibacter.saccharivorans
## 2025-03-22 22:11:26.930645 INFO::Fitting model to feature number 10, species.Flavonifractor.plautii
## 2025-03-22 22:11:26.932949 INFO::Fitting model to feature number 11, species.Dialister.invisus
## 2025-03-22 22:11:26.936175 INFO::Fitting model to feature number 12, species.Ruminococcus.bicirculans
## 2025-03-22 22:11:26.938578 INFO::Fitting model to feature number 13, species.Blautia.sp..CAG.257
## 2025-03-22 22:11:26.940871 INFO::Fitting model to feature number 14, species..Ruminococcus..gnavus
## 2025-03-22 22:11:26.943157 INFO::Fitting model to feature number 15, species.Dorea.longicatena
## 2025-03-22 22:11:26.945426 INFO::Fitting model to feature number 16, species.Anaerobutyricum.hallii
## 2025-03-22 22:11:26.947766 INFO::Fitting model to feature number 17, species.Enterocloster.bolteae
## 2025-03-22 22:11:26.950025 INFO::Fitting model to feature number 18, species.Eubacterium.sp..CAG.38
## 2025-03-22 22:11:26.952309 INFO::Fitting model to feature number 19, species.Lacrimispora.saccharolytica
## 2025-03-22 22:11:26.976979 INFO::Fitting model to feature number 20, species.Intestinimonas.butyriciproducens
## 2025-03-22 22:11:26.980368 INFO::Fitting model to feature number 21, species.Anaerostipes.hadrus
## 2025-03-22 22:11:26.982667 INFO::Fitting model to feature number 22, species.Anaerotignum.lactatifermentans
## 2025-03-22 22:11:26.984954 INFO::Fitting model to feature number 23, species.Ruthenibacterium.lactatiformans
## 2025-03-22 22:11:26.987207 INFO::Fitting model to feature number 24, species.Lawsonibacter.asaccharolyticus
## 2025-03-22 22:11:26.989446 INFO::Fitting model to feature number 25, species.Clostridium.bolteae.CAG.59
## 2025-03-22 22:11:26.991703 INFO::Fitting model to feature number 26, species..Clostridium..symbiosum
## 2025-03-22 22:11:26.99395 INFO::Fitting model to feature number 27, species.Anaerotruncus.colihominis
## 2025-03-22 22:11:26.996194 INFO::Fitting model to feature number 28, species.Agathobaculum.butyriciproducens
## 2025-03-22 22:11:26.998447 INFO::Fitting model to feature number 29, species.Escherichia.coli
## 2025-03-22 22:11:27.001563 INFO::Fitting model to feature number 30, species.Eisenbergiella.massiliensis
## 2025-03-22 22:11:27.004009 INFO::Fitting model to feature number 31, species.Enterocloster.citroniae
## 2025-03-22 22:11:27.006298 INFO::Fitting model to feature number 32, species.Bacteroides.stercoris
## 2025-03-22 22:11:27.008605 INFO::Fitting model to feature number 33, species.Monoglobus.pectinilyticus
## 2025-03-22 22:11:27.010846 INFO::Fitting model to feature number 34, species.Alistipes.putredinis
## 2025-03-22 22:11:27.013099 INFO::Fitting model to feature number 35, species.Parabacteroides.distasonis
## 2025-03-22 22:11:27.015351 INFO::Fitting model to feature number 36, species.Roseburia.hominis
## 2025-03-22 22:11:27.017607 INFO::Fitting model to feature number 37, species.Bifidobacterium.longum
## 2025-03-22 22:11:27.019867 INFO::Fitting model to feature number 38, species..Eubacterium..siraeum
## 2025-03-22 22:11:27.022137 INFO::Fitting model to feature number 39, species.Parabacteroides.merdae
## 2025-03-22 22:11:27.025354 INFO::Fitting model to feature number 40, species.Roseburia.inulinivorans
## 2025-03-22 22:11:27.027636 INFO::Fitting model to feature number 41, species.Bacteroides.cellulosilyticus
## 2025-03-22 22:11:27.029919 INFO::Fitting model to feature number 42, species.Bacteroides.ovatus
## 2025-03-22 22:11:27.032155 INFO::Fitting model to feature number 43, species.Blautia.wexlerae
## 2025-03-22 22:11:27.034399 INFO::Fitting model to feature number 44, species.Bifidobacterium.adolescentis
## 2025-03-22 22:11:27.036698 INFO::Fitting model to feature number 45, species.Lachnospira.eligens
## 2025-03-22 22:11:27.038938 INFO::Fitting model to feature number 46, species..Clostridium..leptum
## 2025-03-22 22:11:27.041196 INFO::Fitting model to feature number 47, species.Eggerthella.lenta
## 2025-03-22 22:11:27.043422 INFO::Fitting model to feature number 48, species.Bacteroides.xylanisolvens
## 2025-03-22 22:11:27.046649 INFO::Fitting model to feature number 49, species.Phocaeicola.dorei
## 2025-03-22 22:11:27.048888 INFO::Fitting model to feature number 50, species.Enterocloster.lavalensis
## 2025-03-22 22:11:27.051117 INFO::Fitting model to feature number 51, species..Eubacterium..rectale
## 2025-03-22 22:11:27.053362 INFO::Fitting model to feature number 52, species.Akkermansia.muciniphila
## 2025-03-22 22:11:27.055621 INFO::Fitting model to feature number 53, species.Acidaminococcus.intestini
## 2025-03-22 22:11:27.058744 INFO::Fitting model to feature number 54, species..Ruminococcus..torques
## 2025-03-22 22:11:27.061511 INFO::Fitting model to feature number 55, species.Bacteroides.salyersiae
## 2025-03-22 22:11:27.063796 INFO::Fitting model to feature number 56, species.Sellimonas.intestinalis
## 2025-03-22 22:11:27.066089 INFO::Fitting model to feature number 57, species.Bacteroides.faecis
## 2025-03-22 22:11:27.069336 INFO::Fitting model to feature number 58, species.Roseburia.intestinalis
## 2025-03-22 22:11:27.071637 INFO::Fitting model to feature number 59, species.Collinsella.aerofaciens
## 2025-03-22 22:11:27.073886 INFO::Fitting model to feature number 60, species.Bacteroides.intestinalis
## 2025-03-22 22:11:27.076163 INFO::Fitting model to feature number 61, species.Bacteroides.faecis.CAG.32
## 2025-03-22 22:11:27.078443 INFO::Fitting model to feature number 62, species..Ruminococcus..lactaris
## 2025-03-22 22:11:27.080733 INFO::Fitting model to feature number 63, species.Prevotella.copri
## 2025-03-22 22:11:27.083031 INFO::Fitting model to feature number 64, species.Eisenbergiella.tayi
## 2025-03-22 22:11:27.085346 INFO::Fitting model to feature number 65, species.Klebsiella.pneumoniae
## 2025-03-22 22:11:27.087643 INFO::Fitting model to feature number 66, species.Intestinibacter.bartlettii
## 2025-03-22 22:11:27.090868 INFO::Fitting model to feature number 67, species.Erysipelatoclostridium.ramosum
## 2025-03-22 22:11:27.093136 INFO::Fitting model to feature number 68, species.Barnesiella.intestinihominis
## 2025-03-22 22:11:27.095432 INFO::Fitting model to feature number 69, species.Blautia.obeum
## 2025-03-22 22:11:27.097713 INFO::Fitting model to feature number 70, species.Bacteroides.finegoldii
## 2025-03-22 22:11:27.09996 INFO::Fitting model to feature number 71, species.Parasutterella.excrementihominis
## 2025-03-22 22:11:27.102343 INFO::Fitting model to feature number 72, species.Phascolarctobacterium.faecium
## 2025-03-22 22:11:27.104702 INFO::Fitting model to feature number 73, species.Lachnospira.pectinoschiza
## 2025-03-22 22:11:27.106971 INFO::Fitting model to feature number 74, species.Clostridium.sp..CAG.58
## 2025-03-22 22:11:27.109251 INFO::Fitting model to feature number 75, species.Bilophila.wadsworthia
## 2025-03-22 22:11:27.112415 INFO::Fitting model to feature number 76, species.Turicimonas.muris
## 2025-03-22 22:11:27.114738 INFO::Fitting model to feature number 77, species.Proteobacteria.bacterium.CAG.139
## 2025-03-22 22:11:27.117007 INFO::Fitting model to feature number 78, species.Anaeromassilibacillus.sp..An250
## 2025-03-22 22:11:27.119299 INFO::Fitting model to feature number 79, species.Hungatella.hathewayi
## 2025-03-22 22:11:27.121639 INFO::Fitting model to feature number 80, species.Alistipes.finegoldii
## 2025-03-22 22:11:27.123928 INFO::Fitting model to feature number 81, species.Ruminococcus.bromii
## 2025-03-22 22:11:27.126201 INFO::Fitting model to feature number 82, species.Odoribacter.splanchnicus
## 2025-03-22 22:11:27.128454 INFO::Fitting model to feature number 83, species.Butyricimonas.virosa
## 2025-03-22 22:11:27.13074 INFO::Fitting model to feature number 84, species.Oscillibacter.sp..CAG.241
## 2025-03-22 22:11:27.133386 INFO::Fitting model to feature number 85, species.Alistipes.indistinctus
## 2025-03-22 22:11:27.136235 INFO::Fitting model to feature number 86, species.Coprococcus.comes
## 2025-03-22 22:11:27.138567 INFO::Fitting model to feature number 87, species.Gemmiger.formicilis
## 2025-03-22 22:11:27.14084 INFO::Fitting model to feature number 88, species.Holdemania.filiformis
## 2025-03-22 22:11:27.143129 INFO::Fitting model to feature number 89, species.Firmicutes.bacterium.CAG.83
## 2025-03-22 22:11:27.145414 INFO::Fitting model to feature number 90, species.Dorea.formicigenerans
## 2025-03-22 22:11:27.14772 INFO::Fitting model to feature number 91, species.Collinsella.intestinalis
## 2025-03-22 22:11:27.150012 INFO::Fitting model to feature number 92, species.Oscillibacter.sp..57_20
## 2025-03-22 22:11:27.152279 INFO::Fitting model to feature number 93, species.Firmicutes.bacterium.CAG.94
## 2025-03-22 22:11:27.154558 INFO::Fitting model to feature number 94, species.Dielma.fastidiosa
## 2025-03-22 22:11:27.157803 INFO::Fitting model to feature number 95, species.Roseburia.sp..CAG.471
## 2025-03-22 22:11:27.160602 INFO::Fitting model to feature number 96, species..Clostridium..innocuum
## 2025-03-22 22:11:27.163779 INFO::Fitting model to feature number 97, species.Haemophilus.parainfluenzae
## 2025-03-22 22:11:27.166184 INFO::Fitting model to feature number 98, species.Veillonella.dispar
## 2025-03-22 22:11:27.168944 INFO::Fitting model to feature number 99, species.Veillonella.parvula
## 2025-03-22 22:11:27.171311 INFO::Fitting model to feature number 100, species.Veillonella.infantium
## 2025-03-22 22:11:27.173634 INFO::Fitting model to feature number 101, species.Streptococcus.salivarius
## 2025-03-22 22:11:27.175934 INFO::Fitting model to feature number 102, species.Enterocloster.aldenensis
## 2025-03-22 22:11:27.179193 INFO::Fitting model to feature number 103, species.Veillonella.atypica
## 2025-03-22 22:11:27.181521 INFO::Fitting model to feature number 104, species.Phocaeicola.plebeius
## 2025-03-22 22:11:27.183829 INFO::Fitting model to feature number 105, species.Paraprevotella.xylaniphila
## 2025-03-22 22:11:27.186102 INFO::Fitting model to feature number 106, species.Bacteroides.eggerthii
## 2025-03-22 22:11:27.188421 INFO::Fitting model to feature number 107, species.Alistipes.shahii
## 2025-03-22 22:11:27.190789 INFO::Fitting model to feature number 108, species.Butyricimonas.synergistica
## 2025-03-22 22:11:27.193062 INFO::Fitting model to feature number 109, species.Haemophilus.sp..HMSC71H05
## 2025-03-22 22:11:27.195391 INFO::Fitting model to feature number 110, species.Eubacterium.ramulus
## 2025-03-22 22:11:27.197746 INFO::Fitting model to feature number 111, species.Coprobacter.fastidiosus
## 2025-03-22 22:11:27.200938 INFO::Fitting model to feature number 112, species.Lactobacillus.rogosae
## 2025-03-22 22:11:27.203242 INFO::Fitting model to feature number 113, species.Phocaeicola.massiliensis
## 2025-03-22 22:11:27.205532 INFO::Fitting model to feature number 114, species.Streptococcus.parasanguinis
## 2025-03-22 22:11:27.207785 INFO::Fitting model to feature number 115, species.Ruminococcaceae.bacterium.D16
## 2025-03-22 22:11:27.210044 INFO::Fitting model to feature number 116, species.Veillonella.sp..T11011.6
## 2025-03-22 22:11:27.212297 INFO::Fitting model to feature number 117, species.Klebsiella.variicola
## 2025-03-22 22:11:27.214578 INFO::Fitting model to feature number 118, species.Bacteroides.galacturonicus
## 2025-03-22 22:11:27.216852 INFO::Fitting model to feature number 119, species.Clostridium.sp..CAG.299
## 2025-03-22 22:11:27.219128 INFO::Fitting model to feature number 120, species.Eubacterium.ventriosum
## 2025-03-22 22:11:27.222378 INFO::Fitting model to feature number 121, species.Bifidobacterium.bifidum
## 2025-03-22 22:11:27.224666 INFO::Fitting model to feature number 122, species.Bifidobacterium.pseudocatenulatum
## 2025-03-22 22:11:27.226942 INFO::Fitting model to feature number 123, species.Coprococcus.eutactus
## 2025-03-22 22:11:27.229308 INFO::Fitting model to feature number 124, species.Eubacterium.sp..CAG.251
## 2025-03-22 22:11:27.231718 INFO::Fitting model to feature number 125, species.Phocaeicola.coprocola
## 2025-03-22 22:11:27.234036 INFO::Fitting model to feature number 126, species.Paraprevotella.clara
## 2025-03-22 22:11:27.236331 INFO::Fitting model to feature number 127, species.Coprococcus.catus
## 2025-03-22 22:11:27.258248 INFO::Counting total values for each feature
## 2025-03-22 22:11:27.272084 INFO::Writing filtered data to file output_species/features/filtered_data.tsv
## 2025-03-22 22:11:27.281036 INFO::Writing filtered, normalized data to file output_species/features/filtered_data_norm.tsv
## 2025-03-22 22:11:27.290234 INFO::Writing filtered, normalized, transformed data to file output_species/features/filtered_data_norm_transformed.tsv
## 2025-03-22 22:11:27.302829 INFO::Writing residuals to file output_species/fits/residuals.rds
## 2025-03-22 22:11:27.308218 INFO::Writing fitted values to file output_species/fits/fitted.rds
## 2025-03-22 22:11:27.313907 INFO::Writing all results to file (ordered by increasing q-values): output_species/all_results.tsv
## 2025-03-22 22:11:27.316319 INFO::Writing the significant results (those which are less than or equal to the threshold of 0.250000 ) to file (ordered by increasing q-values): output_species/significant_results.tsv
## 2025-03-22 22:11:27.31716 INFO::Writing heatmap of significant results to file: output_species/heatmap.pdf
## 2025-03-22 22:11:27.431522 INFO::Writing association plots (one for each significant association) to output folder: output_species
## 2025-03-22 22:11:27.434259 INFO::Plotting associations from most to least significant, grouped by metadata
## 2025-03-22 22:11:27.43484 INFO::Plotting data for metadata number 1, age
## 2025-03-22 22:11:27.435781 INFO::Creating scatter plot for continuous data, age vs species.Alistipes.indistinctus
## 2025-03-22 22:11:27.591894 INFO::Creating scatter plot for continuous data, age vs species.Ruminococcus.bicirculans
## 2025-03-22 22:11:27.802091 INFO::Creating scatter plot for continuous data, age vs species.Lacrimispora.saccharolytica
## 2025-03-22 22:11:27.997508 INFO::Creating scatter plot for continuous data, age vs species.Ruminococcus.bromii
## 2025-03-22 22:11:28.132095 INFO::Creating scatter plot for continuous data, age vs species.Bifidobacterium.pseudocatenulatum
## 2025-03-22 22:11:28.273588 INFO::Creating scatter plot for continuous data, age vs species..Ruminococcus..gnavus
## 2025-03-22 22:11:28.410845 INFO::Creating scatter plot for continuous data, age vs species.Lachnospira.eligens
## 2025-03-22 22:11:28.56423 INFO::Creating scatter plot for continuous data, age vs species.Haemophilus.parainfluenzae
## 2025-03-22 22:11:28.705778 INFO::Creating scatter plot for continuous data, age vs species.Butyricimonas.virosa
## 2025-03-22 22:11:28.843715 INFO::Creating scatter plot for continuous data, age vs species.Lawsonibacter.asaccharolyticus
## 2025-03-22 22:11:28.983571 INFO::Creating scatter plot for continuous data, age vs species..Eubacterium..siraeum
## 2025-03-22 22:11:29.122981 INFO::Creating scatter plot for continuous data, age vs species.Butyricimonas.synergistica
## 2025-03-22 22:11:29.274706 INFO::Creating scatter plot for continuous data, age vs species.Monoglobus.pectinilyticus
## 2025-03-22 22:11:29.411487 INFO::Creating scatter plot for continuous data, age vs species.Veillonella.atypica
## 2025-03-22 22:11:31.119495 INFO::Plotting data for metadata number 2, disease
## 2025-03-22 22:11:31.121364 INFO::Creating boxplot for categorical data, disease vs species.Alistipes.putredinis
## 2025-03-22 22:11:31.287487 INFO::Creating boxplot for categorical data, disease vs species.Gemmiger.formicilis
## 2025-03-22 22:11:31.427276 INFO::Creating boxplot for categorical data, disease vs species..Ruminococcus..torques
## 2025-03-22 22:11:31.571056 INFO::Creating boxplot for categorical data, disease vs species.Ruminococcus.bicirculans
## 2025-03-22 22:11:31.695919 INFO::Creating boxplot for categorical data, disease vs species.Sellimonas.intestinalis
## 2025-03-22 22:11:31.820259 INFO::Creating boxplot for categorical data, disease vs species..Clostridium..leptum
## 2025-03-22 22:11:31.945372 INFO::Creating boxplot for categorical data, disease vs species.Alistipes.shahii
## 2025-03-22 22:11:33.123301 INFO::Plotting data for metadata number 3, antibiotics_current_use
## 2025-03-22 22:11:33.124607 INFO::Creating boxplot for categorical data, antibiotics_current_use vs species.Coprobacter.fastidiosus
## 2025-03-22 22:11:33.251568 INFO::Creating boxplot for categorical data, antibiotics_current_use vs species..Eubacterium..rectale
## 2025-03-22 22:11:33.381449 INFO::Creating boxplot for categorical data, antibiotics_current_use vs species.Agathobaculum.butyriciproducensUnlike gene expression studies, we do not have well-defined signatures or modules for microbiome data. Here, we will construct data-driven modules using weighted gene co-expression network analysis (WGCNA) (Langfelder and Horvath 2008), (Geistlinger et al. 2023). We aim to ensure that the effect of disease and other covariates has been removed by working on the residuals. Following the WGCNA tutorial, our first step will be to check whether there are any outliers in our data.
Langfelder, Peter, and Steve Horvath. 2008. “WGCNA: An r Package for Weighted Correlation Network Analysis.” BMC Bioinformatics 9: 559. https://doi.org/https://doi.org/10.1186/1471-2105-9-559.
Geistlinger, Ludwig, Chloe Mirzayi, Fatima Zohra, Rimsha Azhar, Shaimaa Elsafoury, Clare Grieve, Jennifer Wokaty, et al. 2023. “BugSigDB Captures Patterns of Differential Abundance Across a Broad Range of Host-Associated Microbial Signatures.” Nature Biotechnology 42 (5): 790–802. https://doi.org/https://doi.org/10.1038/s41587-023-01872-y.
library(WGCNA)
datExpr <- as.data.frame(t(fit_data$residuals))
gsg = goodSamplesGenes(datExpr, verbose = 3)
## Flagging genes and samples with too many missing values...
## ..step 1
## ..Excluding 6 samples from the calculation due to too many missing genes.
## ..step 2
gsg$allOK
## [1] FALSEIf the last statement returns TRUE, no outliers are identified. If not, we need to remove the outliers from the data.
if (!gsg$allOK)
{if (sum(!gsg$goodGenes) > 0)
printFlush(paste(
"Removing genes:",
paste(names(datExpr)[!gsg$goodGenes], collapse = ", ")));
if (sum(!gsg$goodSamples) > 0)
printFlush(paste(
"Removing samples:",
paste(rownames(datExpr)[!gsg$goodSamples], collapse =", ")))
datExpr = datExpr[gsg$goodSamples, gsg$goodGenes]
}
## Removing samples: CSM5MCVB_P, CSM79HNY_P, ESM5GEYY_P, ESM718U9_P, MSM6J2N6_P, MSM9VZLX_PAfter removing the outliers, we need to choose a suitable soft threshold parameter for creating the modules as part of the WGCNA algorithm. This power value must produce a graph similar to a scale-free network. We can use the mean connectivity graphic for the selection of this power parameter.
# Choose a set of soft threshold parameters
powers = c(c(1:20), seq(from = 22, to=30, by=2))
sft = pickSoftThreshold(
datExpr, powerVector = powers, verbose = 5, dataIsExpr = TRUE,
RsquaredCut = 0.30)
## pickSoftThreshold: will use block size 127.
## pickSoftThreshold: calculating connectivity for given powers...
## ..working on genes 1 through 127 of 127
## Power SFT.R.sq slope truncated.R.sq mean.k. median.k. max.k.
## 1 1 0.1790 -0.972 0.85700 15.00000 1.48e+01 23.0000
## 2 2 0.3450 -0.729 0.63500 2.95000 2.85e+00 5.6900
## 3 3 0.2400 -4.130 0.12700 0.80400 7.36e-01 2.6100
## 4 4 0.3100 -4.870 0.19900 0.29200 2.14e-01 1.6700
## 5 5 0.2150 -4.030 -0.00880 0.13700 7.02e-02 1.2200
## 6 6 0.1800 -2.930 -0.05130 0.07910 2.46e-02 0.9570
## 7 7 0.1380 -2.240 -0.10100 0.05320 9.33e-03 0.7900
## 8 8 0.2200 -2.790 -0.00259 0.03940 3.71e-03 0.6690
## 9 9 0.0872 -1.450 -0.09130 0.03100 1.50e-03 0.5760
## 10 10 0.1190 -1.630 -0.07660 0.02540 6.73e-04 0.5020
## 11 11 0.0562 -1.250 -0.03470 0.02130 2.66e-04 0.4410
## 12 12 0.1620 -2.150 -0.07720 0.01810 1.12e-04 0.3910
## 13 13 0.2120 -2.350 -0.00949 0.01560 4.84e-05 0.3480
## 14 14 0.2480 -2.410 0.04950 0.01360 2.12e-05 0.3110
## 15 15 0.2890 -2.470 0.15200 0.01190 9.53e-06 0.2810
## 16 16 0.3030 -2.420 0.18400 0.01050 4.33e-06 0.2580
## 17 17 0.2410 -2.380 0.02450 0.00933 1.98e-06 0.2380
## 18 18 0.3190 -2.640 0.15400 0.00830 9.03e-07 0.2180
## 19 19 0.3320 -2.600 0.17700 0.00741 4.03e-07 0.2010
## 20 20 0.2370 -2.050 0.02180 0.00664 1.70e-07 0.1840
## 21 22 0.2350 -2.000 0.07520 0.00536 3.40e-08 0.1560
## 22 24 0.2430 -2.230 0.09560 0.00437 6.98e-09 0.1310
## 23 26 0.2370 -2.120 0.26200 0.00358 1.44e-09 0.1110
## 24 28 0.2490 -2.080 0.26200 0.00294 2.93e-10 0.0937
## 25 30 0.2490 -2.290 0.30100 0.00243 5.67e-11 0.0791In this step, we will conduct a one-step module detection based on the selected soft threshold parameter selected above.
power = sft$powerEstimate
net = blockwiseModules(
datExpr,
power = power,
corFnc="bicor",
corOptions=list(maxPOutliers=0.1),
networkType ="unsigned",
maxBlockSize = ncol(datExpr),
minModuleSize = 3,
TOMType = "unsigned",
reassignThreshold = 0,
mergeCutHeight = 0,
verbose = 3)
## Calculating module eigengenes block-wise from all genes
## Flagging genes and samples with too many missing values...
## ..step 1
## ..Working on block 1 .
## TOM calculation: adjacency..
## ..will not use multithreading.
## Fraction of slow calculations: 0.000000
## ..connectivity..
## ..matrix multiplication (system BLAS)..
## ..normalization..
## ..done.
## ....clustering..
## ....detecting modules..
## ....calculating module eigengenes..
## ....checking kME in modules..
## ..removing 3 genes from module 1 because their KME is too low.
## ..removing 3 genes from module 2 because their KME is too low.
## ..removing 2 genes from module 3 because their KME is too low.
## ..removing 1 genes from module 5 because their KME is too low.
## ..removing 1 genes from module 7 because their KME is too low.
## ..merging modules that are too close..
## mergeCloseModules: Merging modules whose distance is less than 0
## Calculating new MEs...
####################
# How many modules #
####################
ncol(net$MEs)
## [1] 14
table(net$colors)
##
## black blue brown green greenyellow grey
## 7 14 13 12 5 10
## magenta pink purple red salmon tan
## 6 6 5 11 3 5
## turquoise yellow
## 18 12The WGCNA algorithm produced 14 modules which we can visualize as follows.
##########################
# Plot module dendrogram #
##########################
eigenGenes <- net$MEs
MEDiss = 1-cor(eigenGenes)
METree = hclust(as.dist(MEDiss), method = "average")
plot(METree, main = "Clustering of module eigengenes", xlab = "", sub = "")
Next, we calculate hub genes for the modules and create the mapping files to proceed with the MSEA.
###########################################
# Re-calculate modules and find hub genes #
###########################################
moduleColors <- net$colors
MEs0 = moduleEigengenes(datExpr, moduleColors)$eigengenes
modules_data = orderMEs(MEs0)
#######################
# Create mapping file #
#######################
library(tidyverse)
feature_by_modules <- as.data.frame(net$colors)
feature_by_modules <- rownames_to_column(feature_by_modules)
colnames(feature_by_modules) <- c('Feature', 'Module')
features_mapping <- feature_by_modules
features_mapping$Module <- paste('ME', features_mapping$Module, sep = '')Finally, we will run the MSEA analysis on the modules we constructed using WGCNA. Here, we first create a wrapper for the MSEA analysis using the gsEasy package.
library(reshape2)
library(gsEasy)
################
# MSEA Wrapper #
################
run_MSEA <- function(
microbeSet, # A list
ranked_features, # Ranked list of featured
filter.count = 3,
seed = 1234,
fdr.correction = 'BH') {
###################
# Filter out sets #
##################
microbeSet0 <- microbeSet
cond <- sapply(microbeSet0, function(x) length(x) > filter.count)
microbeSet <- microbeSet0[cond]
lengthmicrobeSet <- as.data.frame(
reshape2::melt(lapply(microbeSet, function(x) length(x))))
colnames(lengthmicrobeSet) <- c('Freq','Set')
################
# Classic MSEA #
################
set.seed(seed)
enrichment <- as.data.frame(
sapply(microbeSet, function(set) gset(S = set, r = ranked_features)))
colnames(enrichment)<-'ES'
enrichment <- rownames_to_column(enrichment, 'Set')
enrichment <- merge(enrichment, lengthmicrobeSet, 'Set')
enrichment$qval <- p.adjust(enrichment$ES, fdr.correction)
##########
# Return #
##########
return(enrichment)
}Before running the MSEA, we also need to rank the differential analysis results from MaAsLin2. We use the topGo package to create a list of microbe sets from the mapping file created above.
###################
# Rank DA results #
###################
results <- fit_data$results |> filter(metadata == 'disease')
results$qval <- p.adjust(results$pval, 'BH')
results <- results[order(results$qval, decreasing = FALSE), ]
###################
# MSEA Processing #
###################
library(topGO)
module_map <- features_mapping
mod.gs <- tapply(module_map$Module, module_map$Feature, as.character)
microbeSet <- inverseList(mod.gs)
microbeSet
## $MEblack
## [1] "species.Anaeromassilibacillus.sp..An250"
## [2] "species.Anaerotruncus.colihominis"
## [3] "species.Blautia.wexlerae"
## [4] "species.Eisenbergiella.tayi"
## [5] "species.Firmicutes.bacterium.CAG.94"
## [6] "species.Ruthenibacterium.lactatiformans"
## [7] "species.Sellimonas.intestinalis"
##
## $MEblue
## [1] "species.Clostridium.sp..CAG.58"
## [2] "species.Erysipelatoclostridium.ramosum"
## [3] "species.Haemophilus.parainfluenzae"
## [4] "species.Intestinibacter.bartlettii"
## [5] "species.Klebsiella.pneumoniae"
## [6] "species.Klebsiella.variicola"
## [7] "species.Lawsonibacter.asaccharolyticus"
## [8] "species.Streptococcus.parasanguinis"
## [9] "species.Streptococcus.salivarius"
## [10] "species.Veillonella.atypica"
## [11] "species.Veillonella.dispar"
## [12] "species.Veillonella.infantium"
## [13] "species.Veillonella.parvula"
## [14] "species.Veillonella.sp..T11011.6"
##
## $MEbrown
## [1] "species..Eubacterium..siraeum"
## [2] "species.Alistipes.finegoldii"
## [3] "species.Alistipes.indistinctus"
## [4] "species.Alistipes.putredinis"
## [5] "species.Alistipes.shahii"
## [6] "species.Bacteroides.xylanisolvens"
## [7] "species.Bilophila.wadsworthia"
## [8] "species.Firmicutes.bacterium.CAG.83"
## [9] "species.Odoribacter.splanchnicus"
## [10] "species.Oscillibacter.sp..57_20"
## [11] "species.Oscillibacter.sp..CAG.241"
## [12] "species.Phocaeicola.dorei"
## [13] "species.Ruminococcus.bromii"
##
## $MEgreen
## [1] "species..Clostridium..symbiosum"
## [2] "species.Blautia.sp..CAG.257"
## [3] "species.Clostridium.bolteae.CAG.59"
## [4] "species.Eggerthella.lenta"
## [5] "species.Eisenbergiella.massiliensis"
## [6] "species.Enterocloster.aldenensis"
## [7] "species.Enterocloster.bolteae"
## [8] "species.Enterocloster.citroniae"
## [9] "species.Enterocloster.clostridioformis"
## [10] "species.Enterocloster.lavalensis"
## [11] "species.Flavonifractor.plautii"
## [12] "species.Lacrimispora.saccharolytica"
##
## $MEgreenyellow
## [1] "species..Clostridium..innocuum" "species..Ruminococcus..gnavus"
## [3] "species.Coprobacter.fastidiosus" "species.Escherichia.coli"
## [5] "species.Hungatella.hathewayi"
##
## $MEgrey
## [1] "species.Anaerotignum.lactatifermentans"
## [2] "species.Bacteroides.cellulosilyticus"
## [3] "species.Bacteroides.fragilis"
## [4] "species.Collinsella.intestinalis"
## [5] "species.Eubacterium.sp..CAG.38"
## [6] "species.Haemophilus.sp..HMSC71H05"
## [7] "species.Intestinimonas.butyriciproducens"
## [8] "species.Lachnospira.eligens"
## [9] "species.Roseburia.intestinalis"
## [10] "species.Roseburia.sp..CAG.471"
##
## $MEmagenta
## [1] "species.Bacteroides.finegoldii" "species.Paraprevotella.clara"
## [3] "species.Paraprevotella.xylaniphila" "species.Phocaeicola.coprocola"
## [5] "species.Phocaeicola.plebeius" "species.Prevotella.copri"
##
## $MEpink
## [1] "species.Bacteroides.galacturonicus"
## [2] "species.Bifidobacterium.pseudocatenulatum"
## [3] "species.Eubacterium.sp..CAG.251"
## [4] "species.Lachnospira.pectinoschiza"
## [5] "species.Lactobacillus.rogosae"
## [6] "species.Phocaeicola.massiliensis"
##
## $MEpurple
## [1] "species.Barnesiella.intestinihominis"
## [2] "species.Butyricimonas.synergistica"
## [3] "species.Butyricimonas.virosa"
## [4] "species.Coprococcus.eutactus"
## [5] "species.Ruminococcus.bicirculans"
##
## $MEred
## [1] "species..Clostridium..leptum"
## [2] "species.Akkermansia.muciniphila"
## [3] "species.Bacteroides.intestinalis"
## [4] "species.Clostridium.sp..CAG.299"
## [5] "species.Dialister.invisus"
## [6] "species.Dielma.fastidiosa"
## [7] "species.Holdemania.filiformis"
## [8] "species.Monoglobus.pectinilyticus"
## [9] "species.Parasutterella.excrementihominis"
## [10] "species.Proteobacteria.bacterium.CAG.139"
## [11] "species.Turicimonas.muris"
##
## $MEsalmon
## [1] "species.Bacteroides.faecis"
## [2] "species.Bacteroides.faecis.CAG.32"
## [3] "species.Phascolarctobacterium.faecium"
##
## $MEtan
## [1] "species.Bacteroides.salyersiae"
## [2] "species.Bifidobacterium.adolescentis"
## [3] "species.Bifidobacterium.bifidum"
## [4] "species.Bifidobacterium.longum"
## [5] "species.Collinsella.aerofaciens"
##
## $MEturquoise
## [1] "species..Eubacterium..rectale"
## [2] "species..Ruminococcus..torques"
## [3] "species.Agathobaculum.butyriciproducens"
## [4] "species.Anaerobutyricum.hallii"
## [5] "species.Anaerostipes.hadrus"
## [6] "species.Bacteroides.eggerthii"
## [7] "species.Blautia.obeum"
## [8] "species.Coprococcus.catus"
## [9] "species.Coprococcus.comes"
## [10] "species.Dorea.formicigenerans"
## [11] "species.Dorea.longicatena"
## [12] "species.Eubacterium.ramulus"
## [13] "species.Faecalibacterium.prausnitzii"
## [14] "species.Fusicatenibacter.saccharivorans"
## [15] "species.Gemmiger.formicilis"
## [16] "species.Roseburia.faecis"
## [17] "species.Roseburia.hominis"
## [18] "species.Roseburia.inulinivorans"
##
## $MEyellow
## [1] "species..Ruminococcus..lactaris"
## [2] "species.Acidaminococcus.intestini"
## [3] "species.Bacteroides.caccae"
## [4] "species.Bacteroides.ovatus"
## [5] "species.Bacteroides.stercoris"
## [6] "species.Bacteroides.thetaiotaomicron"
## [7] "species.Bacteroides.uniformis"
## [8] "species.Eubacterium.ventriosum"
## [9] "species.Parabacteroides.distasonis"
## [10] "species.Parabacteroides.merdae"
## [11] "species.Phocaeicola.vulgatus"
## [12] "species.Ruminococcaceae.bacterium.D16"We are now ready to run the MSEA analysis. We run \(100,000\) permutations to calculate the enrichment scores.
We can plot the enrichment scores to visualize the MSEA results.
p <- MSEA |>
arrange(-pval) |>
mutate(ID = factor(ID, levels = ID)) |>
ggplot(aes(y = -log10(pval), x = ID)) +
geom_bar(stat = "identity", fill = 'cornflowerblue') + theme_bw() +
coord_flip() +
ggtitle('Statistically significant modules associated with disease') +
xlab('') +
ylab('MSEA enrichment score')
print(p)
Based on the MSEA results, we obtain 13 enriched modules of microbial species. We can also examine the members of the top enriched modules.
A.3 Print the most significant modules for species relative abundance data
microbeSet[["MEpurple"]]
## [1] "species.Barnesiella.intestinihominis"
## [2] "species.Butyricimonas.synergistica"
## [3] "species.Butyricimonas.virosa"
## [4] "species.Coprococcus.eutactus"
## [5] "species.Ruminococcus.bicirculans"
microbeSet[["MEbrown"]]
## [1] "species..Eubacterium..siraeum"
## [2] "species.Alistipes.finegoldii"
## [3] "species.Alistipes.indistinctus"
## [4] "species.Alistipes.putredinis"
## [5] "species.Alistipes.shahii"
## [6] "species.Bacteroides.xylanisolvens"
## [7] "species.Bilophila.wadsworthia"
## [8] "species.Firmicutes.bacterium.CAG.83"
## [9] "species.Odoribacter.splanchnicus"
## [10] "species.Oscillibacter.sp..57_20"
## [11] "species.Oscillibacter.sp..CAG.241"
## [12] "species.Phocaeicola.dorei"
## [13] "species.Ruminococcus.bromii"A.4 Performing the MSEA analysis with pathway relative abundance data
Next, we repeat the MSEA with the pathway relative abundance data from the iHMP project and follow the same steps as before.
##########################
# Load HMP2 pathway data #
##########################
se_pathway <- sampleMetadata |>
filter(study_name == "HMP_2019_ibdmdb") |>
returnSamples("pathway_abundance", rownames = "short")
##########################
# Create sample metadata #
##########################
sample_metadata <- colData(se_pathway) |>
as.data.frame() |> filter(visit_number == 1) |>
dplyr::select("age", "disease", "antibiotics_current_use")
# Set reference
sample_metadata$disease <- as.factor(sample_metadata$disease)
sample_metadata$disease <- relevel(sample_metadata$disease, 'healthy')
###########################
# Create Pathway Features #
###########################
feature_pwys_t <- as.data.frame(assay(se_pathway))
feature_pwys_t <- rownames_to_column(feature_pwys_t, "ID")
feature_pwys_t <- feature_pwys_t |>
filter(!grepl("\\|", ID)) |>
filter(!ID %in% c('UNMAPPED', 'UNINTEGRATED')) |>
column_to_rownames('ID') |>
as.data.frame()
##############################
# Subset to baseline samples #
##############################
feature_pwys <- as.data.frame(t(feature_pwys_t))
feature_pwys <- feature_pwys[rownames(sample_metadata),]
feature_pwys <- feature_pwys / 100
rm(feature_pwys_t); rm(se_pathway)As before, we first run a MaAsLin2 analysis using default settings and construct the modules using residuals from the MaAsLin2 models.
fit_data = Maaslin2(
input_data = feature_pwys,
input_metadata = sample_metadata,
normalization = "NONE",
output = "output_pwys",
fixed_effects = c("disease", "age", "antibiotics_current_use"))
## [1] "Creating output folder"
## [1] "Creating output feature tables folder"
## [1] "Creating output fits folder"
## [1] "Creating output figures folder"
## 2025-03-22 22:11:59.274362 INFO::Writing function arguments to log file
## 2025-03-22 22:11:59.279182 INFO::Verifying options selected are valid
## 2025-03-22 22:11:59.279731 INFO::Determining format of input files
## 2025-03-22 22:11:59.28023 INFO::Input format is data samples as rows and metadata samples as rows
## 2025-03-22 22:11:59.285879 INFO::Formula for fixed effects: expr ~ disease + age + antibiotics_current_use
## 2025-03-22 22:11:59.286447 INFO::Factor detected for categorial metadata 'disease'. Provide a reference argument or manually set factor ordering to change reference level.
## 2025-03-22 22:11:59.28708 INFO::Filter data based on min abundance and min prevalence
## 2025-03-22 22:11:59.287535 INFO::Total samples in data: 136
## 2025-03-22 22:11:59.287961 INFO::Min samples required with min abundance for a feature not to be filtered: 13.600000
## 2025-03-22 22:11:59.294588 INFO::Total filtered features: 113
## 2025-03-22 22:11:59.295312 INFO::Filtered feature names from abundance and prevalence filtering: PWY.5044..purine.nucleotides.degradation.I..plants., PROPFERM.PWY..L.alanine.fermentation.to.propanoate.and.acetate, PWY.6596..adenosine.nucleotides.degradation.I, PWY.5004..superpathway.of.L.citrulline.metabolism, UDPNACETYLGALSYN.PWY..UDP.N.acetyl.D.glucosamine.biosynthesis.II, PWY66.367..ketogenesis, PWY.5392..reductive.TCA.cycle.II, PWY.101..photosynthesis.light.reactions, PWY.7031..protein.N.glycosylation..bacterial., PWY.5265..peptidoglycan.biosynthesis.II..staphylococci., PWY.7268..NAD.NADP.NADH.NADPH.cytosolic.interconversion..yeast., PWY.7165..L.ascorbate.biosynthesis.VI..engineered.pathway., CATECHOL.ORTHO.CLEAVAGE.PWY..catechol.degradation.to..beta..ketoadipate, PWY.5417..catechol.degradation.III..ortho.cleavage.pathway., PWY.5431..aromatic.compounds.degradation.via..beta..ketoadipate, PWY3DJ.35471..L.ascorbate.biosynthesis.IV, PWY.6185..4.methylcatechol.degradation..ortho.cleavage., PWY.7245..superpathway.NAD.NADP...NADH.NADPH.interconversion..yeast., PWY.5181..toluene.degradation.III..aerobic...via.p.cresol., PWY.6562..norspermidine.biosynthesis, PWY.7431..aromatic.biogenic.amine.degradation..bacteria., PWY.6307..L.tryptophan.degradation.X..mammalian..via.tryptamine., PWY.6313..serotonin.degradation, URSIN.PWY..ureide.biosynthesis, LIPASYN.PWY..phospholipases, DHGLUCONATE.PYR.CAT.PWY..glucose.degradation..oxidative., DENITRIFICATION.PWY..nitrate.reduction.I..denitrification., PWY.6662..superpathway.of.quinolone.and.alkylquinolone.biosynthesis, PWY.6660..2.heptyl.3.hydroxy.4.1H..quinolone.biosynthesis, PWY.6182..superpathway.of.salicylate.degradation, P165.PWY..superpathway.of.purines.degradation.in.plants, PWY66.388..fatty.acid..alpha..oxidation.III, TYRFUMCAT.PWY..L.tyrosine.degradation.I, PWY.5101..L.isoleucine.biosynthesis.II, PWY.6167..flavin.biosynthesis.II..archaea., PWY.6748..nitrate.reduction.VII..denitrification., PWY.7039..phosphatidate.metabolism..as.a.signaling.molecule, VALDEG.PWY..L.valine.degradation.I, PWY.5198..factor.420.biosynthesis, PWY.6215..4.chlorobenzoate.degradation, AEROBACTINSYN.PWY..aerobactin.biosynthesis, P562.PWY..myo.inositol.degradation.I, PWY.7409..phospholipid.remodeling..phosphatidylethanolamine..yeast., PWY.4722..creatinine.degradation.II, PWY.3801..sucrose.degradation.II..sucrose.synthase., PWY.7345..superpathway.of.anaerobic.sucrose.degradation, P125.PWY..superpathway.of..R.R..butanediol.biosynthesis, PWY.5994..palmitate.biosynthesis.I..animals.and.fungi., PWY.4321..L.glutamate.degradation.IV, PWY.7528..L.methionine.salvage.cycle.I..bacteria.and.plants., PWY.4361..S.methyl.5.thio..alpha..D.ribose.1.phosphate.degradation, PWY.1541..superpathway.of.taurine.degradation, PWY.5654..2.amino.3.carboxymuconate.semialdehyde.degradation.to.2.oxopentenoate, PWY.6210..2.aminophenol.degradation, PWY.6071..superpathway.of.phenylethylamine.degradation, PWY0.321..phenylacetate.degradation.I..aerobic., PWY.7200..superpathway.of.pyrimidine.deoxyribonucleoside.salvage, PWY.2221..Entner.Doudoroff.pathway.III..semi.phosphorylative., PWY.6992..1.5.anhydrofructose.degradation, PWY.7294..xylose.degradation.IV, PWY.6145..superpathway.of.sialic.acids.and.CMP.sialic.acids.biosynthesis, PWY.5180..toluene.degradation.I..aerobic...via.o.cresol., PWY.5182..toluene.degradation.II..aerobic...via.4.methylcatechol., PWY.5415..catechol.degradation.I..meta.cleavage.pathway., PWY.6785..hydrogen.production.VIII, PWY.5509..adenosylcobalamin.biosynthesis.from.cobyrinate.a.c.diamide.I, PWY.6641..superpathway.of.sulfolactate.degradation, PWY.7527..L.methionine.salvage.cycle.III, PWY.6396..superpathway.of.2.3.butanediol.biosynthesis, PWY.6467..Kdo.transfer.to.lipid.IVA.III..Chlamydia., X7ALPHADEHYDROX.PWY..cholate.degradation..bacteria..anaerobic., PWY.7374..1.4.dihydroxy.6.naphthoate.biosynthesis.I, PWY.6906..chitin.derivatives.degradation, PWY.5514..UDP.N.acetyl.D.galactosamine.biosynthesis.II, PWY.7317..superpathway.of.dTDP.glucose.derived.O.antigen.building.blocks.biosynthesis, PWY.7218..photosynthetic.3.hydroxybutanoate.biosynthesis..engineered., PHOTOALL.PWY..oxygenic.photosynthesis, PWY.6344..L.ornithine.degradation.II..Stickland.reaction., P621.PWY..nylon.6.oligomer.degradation, PWY.5028..L.histidine.degradation.II, CRNFORCAT.PWY..creatinine.degradation.I, PWY.6269..adenosylcobalamin.salvage.from.cobinamide.II, PWY.7389..superpathway.of.anaerobic.energy.metabolism..invertebrates., PWY.7384..anaerobic.energy.metabolism..invertebrates..mitochondrial., PWY.6165..chorismate.biosynthesis.II..archaea., PWY5F9.12..biphenyl.degradation, PWY.5647..2.nitrobenzoate.degradation.I, PWY.6138..CMP.N.acetylneuraminate.biosynthesis.I..eukaryotes., PWY.5910..superpathway.of.geranylgeranyldiphosphate.biosynthesis.I..via.mevalonate., PWY.922..mevalonate.pathway.I, PWY.6435..4.hydroxybenzoate.biosynthesis.V, PWY3O.1109..superpathway.of.4.hydroxybenzoate.biosynthesis..yeast., PWY.5754..4.hydroxybenzoate.biosynthesis.I..eukaryotes., PWY1G.0..mycothiol.biosynthesis, PWY.1501..mandelate.degradation.I, PWY.6107..chlorosalicylate.degradation, PWY.5534..propylene.degradation, PWY.7118..chitin.degradation.to.ethanol, PWY.7290..Escherichia.coli.serotype.O86.O.antigen.biosynthesis, PWY.181..photorespiration, PWY.1622..formaldehyde.assimilation.I..serine.pathway., CODH.PWY..reductive.acetyl.coenzyme.A.pathway, PWY.6349..CDP.archaeol.biosynthesis, PWY.6174..mevalonate.pathway.II..archaea., PWY.7286..7..3.amino.3.carboxypropyl..wyosine.biosynthesis, METHANOGENESIS.PWY..methanogenesis.from.H2.and.CO2, PWY.7391..isoprene.biosynthesis.II..engineered., PWY.5055..nicotinate.degradation.III, PWY.7399..methylphosphonate.degradation.II, P241.PWY..coenzyme.B.biosynthesis, PWY.5178..toluene.degradation.IV..aerobic...via.catechol., PWY.5420..catechol.degradation.II..meta.cleavage.pathway., PWY.5419..catechol.degradation.to.2.oxopent.4.enoate.II
## 2025-03-22 22:11:59.302458 INFO::Total filtered features with variance filtering: 0
## 2025-03-22 22:11:59.303107 INFO::Filtered feature names from variance filtering:
## 2025-03-22 22:11:59.30358 INFO::Running selected normalization method: NONE
## 2025-03-22 22:11:59.304016 INFO::Applying z-score to standardize continuous metadata
## 2025-03-22 22:11:59.307921 INFO::Running selected transform method: LOG
## 2025-03-22 22:11:59.315142 INFO::Running selected analysis method: LM
## 2025-03-22 22:11:59.3158 INFO::Fitting model to feature number 1, PWY.1042..glycolysis.IV..plant.cytosol.
## 2025-03-22 22:11:59.31852 INFO::Fitting model to feature number 2, DTDPRHAMSYN.PWY..dTDP.L.rhamnose.biosynthesis.I
## 2025-03-22 22:11:59.320849 INFO::Fitting model to feature number 3, PWY.5695..urate.biosynthesis.inosine.5..phosphate.degradation
## 2025-03-22 22:11:59.324098 INFO::Fitting model to feature number 4, PWY.6936..seleno.amino.acid.biosynthesis
## 2025-03-22 22:11:59.326433 INFO::Fitting model to feature number 5, ILEUSYN.PWY..L.isoleucine.biosynthesis.I..from.threonine.
## 2025-03-22 22:11:59.328789 INFO::Fitting model to feature number 6, PWY.7111..pyruvate.fermentation.to.isobutanol..engineered.
## 2025-03-22 22:11:59.331085 INFO::Fitting model to feature number 7, VALSYN.PWY..L.valine.biosynthesis
## 2025-03-22 22:11:59.333429 INFO::Fitting model to feature number 8, PWY.6609..adenine.and.adenosine.salvage.III
## 2025-03-22 22:11:59.335802 INFO::Fitting model to feature number 9, PWY.6737..starch.degradation.V
## 2025-03-22 22:11:59.338151 INFO::Fitting model to feature number 10, PWY.7219..adenosine.ribonucleotides.de.novo.biosynthesis
## 2025-03-22 22:11:59.340448 INFO::Fitting model to feature number 11, PWY0.1586..peptidoglycan.maturation..meso.diaminopimelate.containing.
## 2025-03-22 22:11:59.342774 INFO::Fitting model to feature number 12, ASPASN.PWY..superpathway.of.L.aspartate.and.L.asparagine.biosynthesis
## 2025-03-22 22:11:59.346068 INFO::Fitting model to feature number 13, PWY.5973..cis.vaccenate.biosynthesis
## 2025-03-22 22:11:59.348499 INFO::Fitting model to feature number 14, PWY.7221..guanosine.ribonucleotides.de.novo.biosynthesis
## 2025-03-22 22:11:59.350817 INFO::Fitting model to feature number 15, PWY.5686..UMP.biosynthesis
## 2025-03-22 22:11:59.353194 INFO::Fitting model to feature number 16, X1CMET2.PWY..N10.formyl.tetrahydrofolate.biosynthesis
## 2025-03-22 22:11:59.35581 INFO::Fitting model to feature number 17, PWY.6122..5.aminoimidazole.ribonucleotide.biosynthesis.II
## 2025-03-22 22:11:59.358123 INFO::Fitting model to feature number 18, PWY.6277..superpathway.of.5.aminoimidazole.ribonucleotide.biosynthesis
## 2025-03-22 22:11:59.360448 INFO::Fitting model to feature number 19, PWY.6385..peptidoglycan.biosynthesis.III..mycobacteria.
## 2025-03-22 22:11:59.362754 INFO::Fitting model to feature number 20, PWY.3841..folate.transformations.II
## 2025-03-22 22:11:59.365043 INFO::Fitting model to feature number 21, RIBOSYN2.PWY..flavin.biosynthesis.I..bacteria.and.plants.
## 2025-03-22 22:11:59.368212 INFO::Fitting model to feature number 22, PWY.6387..UDP.N.acetylmuramoyl.pentapeptide.biosynthesis.I..meso.diaminopimelate.containing.
## 2025-03-22 22:11:59.370501 INFO::Fitting model to feature number 23, THISYNARA.PWY..superpathway.of.thiamin.diphosphate.biosynthesis.III..eukaryotes.
## 2025-03-22 22:11:59.372775 INFO::Fitting model to feature number 24, PWY.7663..gondoate.biosynthesis..anaerobic.
## 2025-03-22 22:11:59.375064 INFO::Fitting model to feature number 25, PWY.6386..UDP.N.acetylmuramoyl.pentapeptide.biosynthesis.II..lysine.containing.
## 2025-03-22 22:11:59.377364 INFO::Fitting model to feature number 26, PWY.6700..queuosine.biosynthesis
## 2025-03-22 22:11:59.379648 INFO::Fitting model to feature number 27, PEPTIDOGLYCANSYN.PWY..peptidoglycan.biosynthesis.I..meso.diaminopimelate.containing.
## 2025-03-22 22:11:59.38192 INFO::Fitting model to feature number 28, TRNA.CHARGING.PWY..tRNA.charging
## 2025-03-22 22:11:59.384199 INFO::Fitting model to feature number 29, PWY.6121..5.aminoimidazole.ribonucleotide.biosynthesis.I
## 2025-03-22 22:11:59.386614 INFO::Fitting model to feature number 30, HISTSYN.PWY..L.histidine.biosynthesis
## 2025-03-22 22:11:59.389863 INFO::Fitting model to feature number 31, PWY.7229..superpathway.of.adenosine.nucleotides.de.novo.biosynthesis.I
## 2025-03-22 22:11:59.392148 INFO::Fitting model to feature number 32, PWY.7199..pyrimidine.deoxyribonucleosides.salvage
## 2025-03-22 22:11:59.394425 INFO::Fitting model to feature number 33, PANTO.PWY..phosphopantothenate.biosynthesis.I
## 2025-03-22 22:11:59.39811 INFO::Fitting model to feature number 34, PWY.2942..L.lysine.biosynthesis.III
## 2025-03-22 22:11:59.400417 INFO::Fitting model to feature number 35, PWY.7237..myo...chiro..and.scillo.inositol.degradation
## 2025-03-22 22:11:59.402719 INFO::Fitting model to feature number 36, PWY.6168..flavin.biosynthesis.III..fungi.
## 2025-03-22 22:11:59.405014 INFO::Fitting model to feature number 37, COA.PWY.1..coenzyme.A.biosynthesis.II..mammalian.
## 2025-03-22 22:11:59.40731 INFO::Fitting model to feature number 38, PWY.5667..CDP.diacylglycerol.biosynthesis.I
## 2025-03-22 22:11:59.409606 INFO::Fitting model to feature number 39, PWY0.1319..CDP.diacylglycerol.biosynthesis.II
## 2025-03-22 22:11:59.412857 INFO::Fitting model to feature number 40, PWY.5097..L.lysine.biosynthesis.VI
## 2025-03-22 22:11:59.415137 INFO::Fitting model to feature number 41, ANAGLYCOLYSIS.PWY..glycolysis.III..from.glucose.
## 2025-03-22 22:11:59.417436 INFO::Fitting model to feature number 42, PWY.6123..inosine.5..phosphate.biosynthesis.I
## 2025-03-22 22:11:59.419731 INFO::Fitting model to feature number 43, ARGININE.SYN4.PWY..L.ornithine.de.novo..biosynthesis
## 2025-03-22 22:11:59.421999 INFO::Fitting model to feature number 44, PWY.6163..chorismate.biosynthesis.from.3.dehydroquinate
## 2025-03-22 22:11:59.424259 INFO::Fitting model to feature number 45, THRESYN.PWY..superpathway.of.L.threonine.biosynthesis
## 2025-03-22 22:11:59.426573 INFO::Fitting model to feature number 46, PYRIDNUCSYN.PWY..NAD.biosynthesis.I..from.aspartate.
## 2025-03-22 22:11:59.428856 INFO::Fitting model to feature number 47, PWY.6124..inosine.5..phosphate.biosynthesis.II
## 2025-03-22 22:11:59.43111 INFO::Fitting model to feature number 48, PWY.6147..6.hydroxymethyl.dihydropterin.diphosphate.biosynthesis.I
## 2025-03-22 22:11:59.434285 INFO::Fitting model to feature number 49, PWY.7539..6.hydroxymethyl.dihydropterin.diphosphate.biosynthesis.III..Chlamydia.
## 2025-03-22 22:11:59.436579 INFO::Fitting model to feature number 50, PWY.6151..S.adenosyl.L.methionine.cycle.I
## 2025-03-22 22:11:59.438855 INFO::Fitting model to feature number 51, SER.GLYSYN.PWY..superpathway.of.L.serine.and.glycine.biosynthesis.I
## 2025-03-22 22:11:59.441121 INFO::Fitting model to feature number 52, PWY.6126..superpathway.of.adenosine.nucleotides.de.novo.biosynthesis.II
## 2025-03-22 22:11:59.4434 INFO::Fitting model to feature number 53, PANTOSYN.PWY..pantothenate.and.coenzyme.A.biosynthesis.I
## 2025-03-22 22:11:59.445737 INFO::Fitting model to feature number 54, PWY.7228..superpathway.of.guanosine.nucleotides.de.novo.biosynthesis.I
## 2025-03-22 22:11:59.448019 INFO::Fitting model to feature number 55, COA.PWY..coenzyme.A.biosynthesis.I
## 2025-03-22 22:11:59.450283 INFO::Fitting model to feature number 56, PWY.4242..pantothenate.and.coenzyme.A.biosynthesis.III
## 2025-03-22 22:11:59.452582 INFO::Fitting model to feature number 57, PWY.6703..preQ0.biosynthesis
## 2025-03-22 22:11:59.455848 INFO::Fitting model to feature number 58, THISYN.PWY..superpathway.of.thiamin.diphosphate.biosynthesis.I
## 2025-03-22 22:11:59.458141 INFO::Fitting model to feature number 59, HISDEG.PWY..L.histidine.degradation.I
## 2025-03-22 22:11:59.460418 INFO::Fitting model to feature number 60, PWY.5659..GDP.mannose.biosynthesis
## 2025-03-22 22:11:59.462709 INFO::Fitting model to feature number 61, PWY.5030..L.histidine.degradation.III
## 2025-03-22 22:11:59.46502 INFO::Fitting model to feature number 62, PWY.5484..glycolysis.II..from.fructose.6.phosphate.
## 2025-03-22 22:11:59.467279 INFO::Fitting model to feature number 63, PWY.3001..superpathway.of.L.isoleucine.biosynthesis.I
## 2025-03-22 22:11:59.469563 INFO::Fitting model to feature number 64, PWY.6125..superpathway.of.guanosine.nucleotides.de.novo.biosynthesis.II
## 2025-03-22 22:11:59.471817 INFO::Fitting model to feature number 65, TRPSYN.PWY..L.tryptophan.biosynthesis
## 2025-03-22 22:11:59.474079 INFO::Fitting model to feature number 66, GLYCOLYSIS..glycolysis.I..from.glucose.6.phosphate.
## 2025-03-22 22:11:59.477336 INFO::Fitting model to feature number 67, PWY.724..superpathway.of.L.lysine..L.threonine.and.L.methionine.biosynthesis.II
## 2025-03-22 22:11:59.479615 INFO::Fitting model to feature number 68, PWY.6897..thiamin.salvage.II
## 2025-03-22 22:11:59.481895 INFO::Fitting model to feature number 69, BRANCHED.CHAIN.AA.SYN.PWY..superpathway.of.branched.amino.acid.biosynthesis
## 2025-03-22 22:11:59.484169 INFO::Fitting model to feature number 70, CALVIN.PWY..Calvin.Benson.Bassham.cycle
## 2025-03-22 22:11:59.486526 INFO::Fitting model to feature number 71, PWY.841..superpathway.of.purine.nucleotides.de.novo.biosynthesis.I
## 2025-03-22 22:11:59.488786 INFO::Fitting model to feature number 72, COMPLETE.ARO.PWY..superpathway.of.aromatic.amino.acid.biosynthesis
## 2025-03-22 22:11:59.491053 INFO::Fitting model to feature number 73, PWY.7220..adenosine.deoxyribonucleotides.de.novo.biosynthesis.II
## 2025-03-22 22:11:59.493308 INFO::Fitting model to feature number 74, PWY.7222..guanosine.deoxyribonucleotides.de.novo.biosynthesis.II
## 2025-03-22 22:11:59.495608 INFO::Fitting model to feature number 75, DENOVOPURINE2.PWY..superpathway.of.purine.nucleotides.de.novo.biosynthesis.II
## 2025-03-22 22:11:59.498231 INFO::Fitting model to feature number 76, PWY.7357..thiamin.formation.from.pyrithiamine.and.oxythiamine..yeast.
## 2025-03-22 22:11:59.502531 INFO::Fitting model to feature number 77, PWY.5103..L.isoleucine.biosynthesis.III
## 2025-03-22 22:11:59.504843 INFO::Fitting model to feature number 78, ARO.PWY..chorismate.biosynthesis.I
## 2025-03-22 22:11:59.507124 INFO::Fitting model to feature number 79, PWY.7282..4.amino.2.methyl.5.phosphomethylpyrimidine.biosynthesis..yeast.
## 2025-03-22 22:11:59.509385 INFO::Fitting model to feature number 80, PWY0.845..superpathway.of.pyridoxal.5..phosphate.biosynthesis.and.salvage
## 2025-03-22 22:11:59.51165 INFO::Fitting model to feature number 81, ANAEROFRUCAT.PWY..homolactic.fermentation
## 2025-03-22 22:11:59.513911 INFO::Fitting model to feature number 82, PWY.6892..thiazole.biosynthesis.I..E..coli.
## 2025-03-22 22:11:59.51618 INFO::Fitting model to feature number 83, RHAMCAT.PWY..L.rhamnose.degradation.I
## 2025-03-22 22:11:59.518445 INFO::Fitting model to feature number 84, PYRIDOXSYN.PWY..pyridoxal.5..phosphate.biosynthesis.I
## 2025-03-22 22:11:59.521711 INFO::Fitting model to feature number 85, PWY.1269..CMP.3.deoxy.D.manno.octulosonate.biosynthesis.I
## 2025-03-22 22:11:59.523958 INFO::Fitting model to feature number 86, PHOSLIPSYN.PWY..superpathway.of.phospholipid.biosynthesis.I..bacteria.
## 2025-03-22 22:11:59.526223 INFO::Fitting model to feature number 87, CITRULBIO.PWY..L.citrulline.biosynthesis
## 2025-03-22 22:11:59.528498 INFO::Fitting model to feature number 88, NAGLIPASYN.PWY..lipid.IVA.biosynthesis
## 2025-03-22 22:11:59.530762 INFO::Fitting model to feature number 89, BIOTIN.BIOSYNTHESIS.PWY..biotin.biosynthesis.I
## 2025-03-22 22:11:59.533008 INFO::Fitting model to feature number 90, PWY.5154..L.arginine.biosynthesis.III..via.N.acetyl.L.citrulline.
## 2025-03-22 22:11:59.535279 INFO::Fitting model to feature number 91, FASYN.ELONG.PWY..fatty.acid.elongation....saturated
## 2025-03-22 22:11:59.537565 INFO::Fitting model to feature number 92, PENTOSE.P.PWY..pentose.phosphate.pathway
## 2025-03-22 22:11:59.539839 INFO::Fitting model to feature number 93, PWYG.321..mycolate.biosynthesis
## 2025-03-22 22:11:59.542932 INFO::Fitting model to feature number 94, PWY.6519..8.amino.7.oxononanoate.biosynthesis.I
## 2025-03-22 22:11:59.545238 INFO::Fitting model to feature number 95, PWY.7664..oleate.biosynthesis.IV..anaerobic.
## 2025-03-22 22:11:59.547534 INFO::Fitting model to feature number 96, PWY.4981..L.proline.biosynthesis.II..from.arginine.
## 2025-03-22 22:11:59.549822 INFO::Fitting model to feature number 97, GLYCOGENSYNTH.PWY..glycogen.biosynthesis.I..from.ADP.D.Glucose.
## 2025-03-22 22:11:59.552083 INFO::Fitting model to feature number 98, PWY.7388..octanoyl..acyl.carrier.protein..biosynthesis..mitochondria..yeast.
## 2025-03-22 22:11:59.55435 INFO::Fitting model to feature number 99, NONOXIPENT.PWY..pentose.phosphate.pathway..non.oxidative.branch.
## 2025-03-22 22:11:59.55663 INFO::Fitting model to feature number 100, COBALSYN.PWY..adenosylcobalamin.salvage.from.cobinamide.I
## 2025-03-22 22:11:59.558896 INFO::Fitting model to feature number 101, PWY.5989..stearate.biosynthesis.II..bacteria.and.plants.
## 2025-03-22 22:11:59.561166 INFO::Fitting model to feature number 102, PWY.6282..palmitoleate.biosynthesis.I..from..5Z..dodec.5.enoate.
## 2025-03-22 22:11:59.563439 INFO::Fitting model to feature number 103, PWY0.862...5Z..dodec.5.enoate.biosynthesis
## 2025-03-22 22:11:59.566748 INFO::Fitting model to feature number 104, PWY.7400..L.arginine.biosynthesis.IV..archaebacteria.
## 2025-03-22 22:11:59.56901 INFO::Fitting model to feature number 105, ARGSYN.PWY..L.arginine.biosynthesis.I..via.L.ornithine.
## 2025-03-22 22:11:59.571269 INFO::Fitting model to feature number 106, PWY.4984..urea.cycle
## 2025-03-22 22:11:59.573552 INFO::Fitting model to feature number 107, FASYN.INITIAL.PWY..superpathway.of.fatty.acid.biosynthesis.initiation..E..coli.
## 2025-03-22 22:11:59.575825 INFO::Fitting model to feature number 108, PWY4FS.7..phosphatidylglycerol.biosynthesis.I..plastidic.
## 2025-03-22 22:11:59.578083 INFO::Fitting model to feature number 109, PWY4FS.8..phosphatidylglycerol.biosynthesis.II..non.plastidic.
## 2025-03-22 22:11:59.580347 INFO::Fitting model to feature number 110, ARGSYNBSUB.PWY..L.arginine.biosynthesis.II..acetyl.cycle.
## 2025-03-22 22:11:59.582616 INFO::Fitting model to feature number 111, PWY.6317..galactose.degradation.I..Leloir.pathway.
## 2025-03-22 22:11:59.584863 INFO::Fitting model to feature number 112, PWY66.422..D.galactose.degradation.V..Leloir.pathway.
## 2025-03-22 22:11:59.588109 INFO::Fitting model to feature number 113, GLUTORN.PWY..L.ornithine.biosynthesis
## 2025-03-22 22:11:59.590354 INFO::Fitting model to feature number 114, PWY.2941..L.lysine.biosynthesis.II
## 2025-03-22 22:11:59.592628 INFO::Fitting model to feature number 115, PWY0.1296..purine.ribonucleosides.degradation
## 2025-03-22 22:11:59.594911 INFO::Fitting model to feature number 116, NAD.BIOSYNTHESIS.II..NAD.salvage.pathway.II
## 2025-03-22 22:11:59.597176 INFO::Fitting model to feature number 117, HSERMETANA.PWY..L.methionine.biosynthesis.III
## 2025-03-22 22:11:59.599428 INFO::Fitting model to feature number 118, PWY0.162..superpathway.of.pyrimidine.ribonucleotides.de.novo.biosynthesis
## 2025-03-22 22:11:59.601897 INFO::Fitting model to feature number 119, PWY.7208..superpathway.of.pyrimidine.nucleobases.salvage
## 2025-03-22 22:11:59.605512 INFO::Fitting model to feature number 120, TEICHOICACID.PWY..teichoic.acid..poly.glycerol..biosynthesis
## 2025-03-22 22:11:59.608091 INFO::Fitting model to feature number 121, PWY.6305..putrescine.biosynthesis.IV
## 2025-03-22 22:11:59.611051 INFO::Fitting model to feature number 122, GLUCONEO.PWY..gluconeogenesis.I
## 2025-03-22 22:11:59.613403 INFO::Fitting model to feature number 123, PWY.621..sucrose.degradation.III..sucrose.invertase.
## 2025-03-22 22:11:59.617191 INFO::Fitting model to feature number 124, PWY.6901..superpathway.of.glucose.and.xylose.degradation
## 2025-03-22 22:11:59.619664 INFO::Fitting model to feature number 125, POLYISOPRENSYN.PWY..polyisoprenoid.biosynthesis..E..coli.
## 2025-03-22 22:11:59.621915 INFO::Fitting model to feature number 126, PWY.7323..superpathway.of.GDP.mannose.derived.O.antigen.building.blocks.biosynthesis
## 2025-03-22 22:11:59.624177 INFO::Fitting model to feature number 127, PWY.5941..glycogen.degradation.II..eukaryotic.
## 2025-03-22 22:11:59.626438 INFO::Fitting model to feature number 128, PWY.6527..stachyose.degradation
## 2025-03-22 22:11:59.628716 INFO::Fitting model to feature number 129, PWY0.1261..anhydromuropeptides.recycling
## 2025-03-22 22:11:59.631871 INFO::Fitting model to feature number 130, PWY66.400..glycolysis.VI..metazoan.
## 2025-03-22 22:11:59.634148 INFO::Fitting model to feature number 131, PWY0.166..superpathway.of.pyrimidine.deoxyribonucleotides.de.novo.biosynthesis..E..coli.
## 2025-03-22 22:11:59.636407 INFO::Fitting model to feature number 132, GLYCOLYSIS.E.D..superpathway.of.glycolysis.and.Entner.Doudoroff
## 2025-03-22 22:11:59.638699 INFO::Fitting model to feature number 133, PWY.7187..pyrimidine.deoxyribonucleotides.de.novo.biosynthesis.II
## 2025-03-22 22:11:59.640973 INFO::Fitting model to feature number 134, PWY.7456..mannan.degradation
## 2025-03-22 22:11:59.643261 INFO::Fitting model to feature number 135, PWY.7184..pyrimidine.deoxyribonucleotides.de.novo.biosynthesis.I
## 2025-03-22 22:11:59.645569 INFO::Fitting model to feature number 136, OANTIGEN.PWY..O.antigen.building.blocks.biosynthesis..E..coli.
## 2025-03-22 22:11:59.647856 INFO::Fitting model to feature number 137, COLANSYN.PWY..colanic.acid.building.blocks.biosynthesis
## 2025-03-22 22:11:59.650138 INFO::Fitting model to feature number 138, PWY.6545..pyrimidine.deoxyribonucleotides.de.novo.biosynthesis.III
## 2025-03-22 22:11:59.653367 INFO::Fitting model to feature number 139, PWY.6895..superpathway.of.thiamin.diphosphate.biosynthesis.II
## 2025-03-22 22:11:59.655754 INFO::Fitting model to feature number 140, PWY.6608..guanosine.nucleotides.degradation.III
## 2025-03-22 22:11:59.65843 INFO::Fitting model to feature number 141, TCA..TCA.cycle.I..prokaryotic.
## 2025-03-22 22:11:59.661232 INFO::Fitting model to feature number 142, PWY.6859..all.trans.farnesol.biosynthesis
## 2025-03-22 22:11:59.665138 INFO::Fitting model to feature number 143, PWY.5100..pyruvate.fermentation.to.acetate.and.lactate.II
## 2025-03-22 22:11:59.668713 INFO::Fitting model to feature number 144, PWY.6572..chondroitin.sulfate.degradation.I..bacterial.
## 2025-03-22 22:11:59.671994 INFO::Fitting model to feature number 145, PWY.6471..peptidoglycan.biosynthesis.IV..Enterococcus.faecium.
## 2025-03-22 22:11:59.675362 INFO::Fitting model to feature number 146, PWY.6470..peptidoglycan.biosynthesis.V...beta..lactam.resistance.
## 2025-03-22 22:11:59.677761 INFO::Fitting model to feature number 147, PWY.5188..tetrapyrrole.biosynthesis.I..from.glutamate.
## 2025-03-22 22:11:59.680047 INFO::Fitting model to feature number 148, GLUCUROCAT.PWY..superpathway.of..beta..D.glucuronide.and.D.glucuronate.degradation
## 2025-03-22 22:11:59.682354 INFO::Fitting model to feature number 149, PWY.6749..CMP.legionaminate.biosynthesis.I
## 2025-03-22 22:11:59.684656 INFO::Fitting model to feature number 150, P164.PWY..purine.nucleobases.degradation.I..anaerobic.
## 2025-03-22 22:11:59.686956 INFO::Fitting model to feature number 151, PWY.7198..pyrimidine.deoxyribonucleotides.de.novo.biosynthesis.IV
## 2025-03-22 22:11:59.689247 INFO::Fitting model to feature number 152, PWY.7211..superpathway.of.pyrimidine.deoxyribonucleotides.de.novo.biosynthesis
## 2025-03-22 22:11:59.691558 INFO::Fitting model to feature number 153, PWY66.409..superpathway.of.purine.nucleotide.salvage
## 2025-03-22 22:11:59.693852 INFO::Fitting model to feature number 154, GALACT.GLUCUROCAT.PWY..superpathway.of.hexuronide.and.hexuronate.degradation
## 2025-03-22 22:11:59.697078 INFO::Fitting model to feature number 155, UDPNAGSYN.PWY..UDP.N.acetyl.D.glucosamine.biosynthesis.I
## 2025-03-22 22:11:59.699457 INFO::Fitting model to feature number 156, PWY.6353..purine.nucleotides.degradation.II..aerobic.
## 2025-03-22 22:11:59.701754 INFO::Fitting model to feature number 157, PWY.7197..pyrimidine.deoxyribonucleotide.phosphorylation
## 2025-03-22 22:11:59.70402 INFO::Fitting model to feature number 158, PWY.7242..D.fructuronate.degradation
## 2025-03-22 22:11:59.707764 INFO::Fitting model to feature number 159, PWY.7196..superpathway.of.pyrimidine.ribonucleosides.salvage
## 2025-03-22 22:11:59.71009 INFO::Fitting model to feature number 160, PWY.5690..TCA.cycle.II..plants.and.fungi.
## 2025-03-22 22:11:59.712356 INFO::Fitting model to feature number 161, PWY.5177..glutaryl.CoA.degradation
## 2025-03-22 22:11:59.714641 INFO::Fitting model to feature number 162, PWY.6478..GDP.D.glycero..alpha..D.manno.heptose.biosynthesis
## 2025-03-22 22:11:59.717046 INFO::Fitting model to feature number 163, HEXITOLDEGSUPER.PWY..superpathway.of.hexitol.degradation..bacteria.
## 2025-03-22 22:11:59.720269 INFO::Fitting model to feature number 164, GALACTUROCAT.PWY..D.galacturonate.degradation.I
## 2025-03-22 22:11:59.722542 INFO::Fitting model to feature number 165, PWY.5104..L.isoleucine.biosynthesis.IV
## 2025-03-22 22:11:59.724799 INFO::Fitting model to feature number 166, PWY.5505..L.glutamate.and.L.glutamine.biosynthesis
## 2025-03-22 22:11:59.727047 INFO::Fitting model to feature number 167, P441.PWY..superpathway.of.N.acetylneuraminate.degradation
## 2025-03-22 22:11:59.729325 INFO::Fitting model to feature number 168, PWY.6606..guanosine.nucleotides.degradation.II
## 2025-03-22 22:11:59.731598 INFO::Fitting model to feature number 169, SALVADEHYPOX.PWY..adenosine.nucleotides.degradation.II
## 2025-03-22 22:11:59.733866 INFO::Fitting model to feature number 170, PWY.5005..biotin.biosynthesis.II
## 2025-03-22 22:11:59.736178 INFO::Fitting model to feature number 171, PWY.6549..L.glutamine.biosynthesis.III
## 2025-03-22 22:11:59.738491 INFO::Fitting model to feature number 172, GLCMANNANAUT.PWY..superpathway.of.N.acetylglucosamine..N.acetylmannosamine.and.N.acetylneuraminate.degradation
## 2025-03-22 22:11:59.741665 INFO::Fitting model to feature number 173, PWY0.1241..ADP.L.glycero..beta..D.manno.heptose.biosynthesis
## 2025-03-22 22:11:59.743993 INFO::Fitting model to feature number 174, PWY.6507..4.deoxy.L.threo.hex.4.enopyranuronate.degradation
## 2025-03-22 22:11:59.746259 INFO::Fitting model to feature number 175, GALACTARDEG.PWY..D.galactarate.degradation.I
## 2025-03-22 22:11:59.748585 INFO::Fitting model to feature number 176, GLUCARGALACTSUPER.PWY..superpathway.of.D.glucarate.and.D.galactarate.degradation
## 2025-03-22 22:11:59.750917 INFO::Fitting model to feature number 177, PWY.5676..acetyl.CoA.fermentation.to.butanoate.II
## 2025-03-22 22:11:59.753188 INFO::Fitting model to feature number 178, PWY.5347..superpathway.of.L.methionine.biosynthesis..transsulfuration.
## 2025-03-22 22:11:59.755492 INFO::Fitting model to feature number 179, PWY.5138..unsaturated..even.numbered.fatty.acid..beta..oxidation
## 2025-03-22 22:11:59.757788 INFO::Fitting model to feature number 180, MET.SAM.PWY..superpathway.of.S.adenosyl.L.methionine.biosynthesis
## 2025-03-22 22:11:59.760077 INFO::Fitting model to feature number 181, PWY66.399..gluconeogenesis.III
## 2025-03-22 22:11:59.763263 INFO::Fitting model to feature number 182, PWY0.1297..superpathway.of.purine.deoxyribonucleosides.degradation
## 2025-03-22 22:11:59.765605 INFO::Fitting model to feature number 183, METSYN.PWY..L.homoserine.and.L.methionine.biosynthesis
## 2025-03-22 22:11:59.767863 INFO::Fitting model to feature number 184, PWY.7332..superpathway.of.UDP.N.acetylglucosamine.derived.O.antigen.building.blocks.biosynthesis
## 2025-03-22 22:11:59.770157 INFO::Fitting model to feature number 185, PWY.6588..pyruvate.fermentation.to.acetone
## 2025-03-22 22:11:59.772457 INFO::Fitting model to feature number 186, PWY.6891..thiazole.biosynthesis.II..Bacillus.
## 2025-03-22 22:11:59.774746 INFO::Fitting model to feature number 187, GLUCARDEG.PWY..D.glucarate.degradation.I
## 2025-03-22 22:11:59.777042 INFO::Fitting model to feature number 188, METH.ACETATE.PWY..methanogenesis.from.acetate
## 2025-03-22 22:11:59.779314 INFO::Fitting model to feature number 189, PWY.7013..L.1.2.propanediol.degradation
## 2025-03-22 22:11:59.78167 INFO::Fitting model to feature number 190, PWY.6590..superpathway.of.Clostridium.acetobutylicum.acidogenic.fermentation
## 2025-03-22 22:11:59.784551 INFO::Fitting model to feature number 191, FAO.PWY..fatty.acid..beta..oxidation.I
## 2025-03-22 22:11:59.787186 INFO::Fitting model to feature number 192, PWY.6318..L.phenylalanine.degradation.IV..mammalian..via.side.chain.
## 2025-03-22 22:11:59.789457 INFO::Fitting model to feature number 193, CENTFERM.PWY..pyruvate.fermentation.to.butanoate
## 2025-03-22 22:11:59.791773 INFO::Fitting model to feature number 194, GOLPDLCAT.PWY..superpathway.of.glycerol.degradation.to.1.3.propanediol
## 2025-03-22 22:11:59.794054 INFO::Fitting model to feature number 195, PWY.5136..fatty.acid..beta..oxidation.II..peroxisome.
## 2025-03-22 22:11:59.796324 INFO::Fitting model to feature number 196, PWY66.391..fatty.acid..beta..oxidation.VI..peroxisome.
## 2025-03-22 22:11:59.798654 INFO::Fitting model to feature number 197, HOMOSER.METSYN.PWY..L.methionine.biosynthesis.I
## 2025-03-22 22:11:59.801009 INFO::Fitting model to feature number 198, METHGLYUT.PWY..superpathway.of.methylglyoxal.degradation
## 2025-03-22 22:11:59.803327 INFO::Fitting model to feature number 199, PWY.7288..fatty.acid..beta..oxidation..peroxisome..yeast.
## 2025-03-22 22:11:59.805879 INFO::Fitting model to feature number 200, PWY.7383..anaerobic.energy.metabolism..invertebrates..cytosol.
## 2025-03-22 22:11:59.810314 INFO::Fitting model to feature number 201, P162.PWY..L.glutamate.degradation.V..via.hydroxyglutarate.
## 2025-03-22 22:11:59.812671 INFO::Fitting model to feature number 202, PWY.4041...gamma..glutamyl.cycle
## 2025-03-22 22:11:59.814943 INFO::Fitting model to feature number 203, P108.PWY..pyruvate.fermentation.to.propanoate.I
## 2025-03-22 22:11:59.817247 INFO::Fitting model to feature number 204, PWY.5022..4.aminobutanoate.degradation.V
## 2025-03-22 22:11:59.819557 INFO::Fitting model to feature number 205, GLUDEG.I.PWY..GABA.shunt
## 2025-03-22 22:11:59.821898 INFO::Fitting model to feature number 206, PWY.5677..succinate.fermentation.to.butanoate
## 2025-03-22 22:11:59.824245 INFO::Fitting model to feature number 207, P163.PWY..L.lysine.fermentation.to.acetate.and.butanoate
## 2025-03-22 22:11:59.826592 INFO::Fitting model to feature number 208, PWY.3781..aerobic.respiration.I..cytochrome.c.
## 2025-03-22 22:11:59.829864 INFO::Fitting model to feature number 209, PWY.5083..NAD.NADH.phosphorylation.and.dephosphorylation
## 2025-03-22 22:11:59.832166 INFO::Fitting model to feature number 210, DAPLYSINESYN.PWY..L.lysine.biosynthesis.I
## 2025-03-22 22:11:59.83449 INFO::Fitting model to feature number 211, P461.PWY..hexitol.fermentation.to.lactate..formate..ethanol.and.acetate
## 2025-03-22 22:11:59.836794 INFO::Fitting model to feature number 212, PWY.1861..formaldehyde.assimilation.II..RuMP.Cycle.
## 2025-03-22 22:11:59.839184 INFO::Fitting model to feature number 213, PWY.7312..dTDP.D..beta..fucofuranose.biosynthesis
## 2025-03-22 22:11:59.841463 INFO::Fitting model to feature number 214, PWY.6630..superpathway.of.L.tyrosine.biosynthesis
## 2025-03-22 22:11:59.843773 INFO::Fitting model to feature number 215, PWY.6595..superpathway.of.guanosine.nucleotides.degradation..plants.
## 2025-03-22 22:11:59.846073 INFO::Fitting model to feature number 216, ARG.POLYAMINE.SYN..superpathway.of.arginine.and.polyamine.biosynthesis
## 2025-03-22 22:11:59.848394 INFO::Fitting model to feature number 217, PWY.7003..glycerol.degradation.to.butanol
## 2025-03-22 22:11:59.851554 INFO::Fitting model to feature number 218, P185.PWY..formaldehyde.assimilation.III..dihydroxyacetone.cycle.
## 2025-03-22 22:11:59.853941 INFO::Fitting model to feature number 219, POLYAMSYN.PWY..superpathway.of.polyamine.biosynthesis.I
## 2025-03-22 22:11:59.856223 INFO::Fitting model to feature number 220, PWY0.1298..superpathway.of.pyrimidine.deoxyribonucleosides.degradation
## 2025-03-22 22:11:59.858597 INFO::Fitting model to feature number 221, LACTOSECAT.PWY..lactose.and.galactose.degradation.I
## 2025-03-22 22:11:59.860914 INFO::Fitting model to feature number 222, PWY4LZ.257..superpathway.of.fermentation..Chlamydomonas.reinhardtii.
## 2025-03-22 22:11:59.863214 INFO::Fitting model to feature number 223, P161.PWY..acetylene.degradation
## 2025-03-22 22:11:59.865539 INFO::Fitting model to feature number 224, RUMP.PWY..formaldehyde.oxidation.I
## 2025-03-22 22:11:59.867847 INFO::Fitting model to feature number 225, PPGPPMET.PWY..ppGpp.biosynthesis
## 2025-03-22 22:11:59.870159 INFO::Fitting model to feature number 226, PWY.5304..superpathway.of.sulfur.oxidation..Acidianus.ambivalens.
## 2025-03-22 22:11:59.8729 INFO::Fitting model to feature number 227, PWY.6531..mannitol.cycle
## 2025-03-22 22:11:59.875739 INFO::Fitting model to feature number 228, FUC.RHAMCAT.PWY..superpathway.of.fucose.and.rhamnose.degradation
## 2025-03-22 22:11:59.878048 INFO::Fitting model to feature number 229, PWY.7315..dTDP.N.acetylthomosamine.biosynthesis
## 2025-03-22 22:11:59.880346 INFO::Fitting model to feature number 230, FUCCAT.PWY..fucose.degradation
## 2025-03-22 22:11:59.882668 INFO::Fitting model to feature number 231, PWY.7210..pyrimidine.deoxyribonucleotides.biosynthesis.from.CTP
## 2025-03-22 22:11:59.885001 INFO::Fitting model to feature number 232, FOLSYN.PWY..superpathway.of.tetrahydrofolate.biosynthesis.and.salvage
## 2025-03-22 22:11:59.887319 INFO::Fitting model to feature number 233, PWY.6612..superpathway.of.tetrahydrofolate.biosynthesis
## 2025-03-22 22:11:59.889662 INFO::Fitting model to feature number 234, PWY0.1061..superpathway.of.L.alanine.biosynthesis
## 2025-03-22 22:11:59.891956 INFO::Fitting model to feature number 235, PWY.5189..tetrapyrrole.biosynthesis.II..from.glycine.
## 2025-03-22 22:11:59.894365 INFO::Fitting model to feature number 236, PWY.6876..isopropanol.biosynthesis
## 2025-03-22 22:11:59.897417 INFO::Fitting model to feature number 237, PWY0.781..aspartate.superpathway
## 2025-03-22 22:11:59.899759 INFO::Fitting model to feature number 238, P4.PWY..superpathway.of.L.lysine..L.threonine.and.L.methionine.biosynthesis.I
## 2025-03-22 22:11:59.902138 INFO::Fitting model to feature number 239, PWY0.1479..tRNA.processing
## 2025-03-22 22:11:59.90449 INFO::Fitting model to feature number 240, GLYCOLYSIS.TCA.GLYOX.BYPASS..superpathway.of.glycolysis..pyruvate.dehydrogenase..TCA..and.glyoxylate.bypass
## 2025-03-22 22:11:59.906811 INFO::Fitting model to feature number 241, PYRIDNUCSAL.PWY..NAD.salvage.pathway.I
## 2025-03-22 22:11:59.909123 INFO::Fitting model to feature number 242, GLYCOCAT.PWY..glycogen.degradation.I..bacterial.
## 2025-03-22 22:11:59.912815 INFO::Fitting model to feature number 243, PWY.5723..Rubisco.shunt
## 2025-03-22 22:11:59.915147 INFO::Fitting model to feature number 244, TCA.GLYOX.BYPASS..superpathway.of.glyoxylate.bypass.and.TCA
## 2025-03-22 22:11:59.918528 INFO::Fitting model to feature number 245, PWY.7385..1.3.propanediol.biosynthesis..engineered.
## 2025-03-22 22:11:59.920903 INFO::Fitting model to feature number 246, PWY.7254..TCA.cycle.VII..acetate.producers.
## 2025-03-22 22:11:59.923207 INFO::Fitting model to feature number 247, GLYOXYLATE.BYPASS..glyoxylate.cycle
## 2025-03-22 22:11:59.925511 INFO::Fitting model to feature number 248, PWY.6731..starch.degradation.III
## 2025-03-22 22:11:59.927805 INFO::Fitting model to feature number 249, PWY.7328..superpathway.of.UDP.glucose.derived.O.antigen.building.blocks.biosynthesis
## 2025-03-22 22:11:59.930121 INFO::Fitting model to feature number 250, POLYAMINSYN3.PWY..superpathway.of.polyamine.biosynthesis.II
## 2025-03-22 22:11:59.932527 INFO::Fitting model to feature number 251, PWY.2723..trehalose.degradation.V
## 2025-03-22 22:11:59.958233 INFO::Fitting model to feature number 252, GLUCOSE1PMETAB.PWY..glucose.and.glucose.1.phosphate.degradation
## 2025-03-22 22:11:59.963152 INFO::Fitting model to feature number 253, PWY.5384..sucrose.degradation.IV..sucrose.phosphorylase.
## 2025-03-22 22:11:59.965489 INFO::Fitting model to feature number 254, PWY.7046..4.coumarate.degradation..anaerobic.
## 2025-03-22 22:11:59.967765 INFO::Fitting model to feature number 255, PWY66.389..phytol.degradation
## 2025-03-22 22:11:59.970018 INFO::Fitting model to feature number 256, PWY.5971..palmitate.biosynthesis.II..bacteria.and.plants.
## 2025-03-22 22:11:59.972285 INFO::Fitting model to feature number 257, PWY.6629..superpathway.of.L.tryptophan.biosynthesis
## 2025-03-22 22:11:59.974577 INFO::Fitting model to feature number 258, PWY.5345..superpathway.of.L.methionine.biosynthesis..by.sulfhydrylation.
## 2025-03-22 22:11:59.976852 INFO::Fitting model to feature number 259, SULFATE.CYS.PWY..superpathway.of.sulfate.assimilation.and.cysteine.biosynthesis
## 2025-03-22 22:11:59.979111 INFO::Fitting model to feature number 260, PWY.5838..superpathway.of.menaquinol.8.biosynthesis.I
## 2025-03-22 22:11:59.981385 INFO::Fitting model to feature number 261, PRPP.PWY..superpathway.of.histidine..purine..and.pyrimidine.biosynthesis
## 2025-03-22 22:11:59.984536 INFO::Fitting model to feature number 262, PWY.5845..superpathway.of.menaquinol.9.biosynthesis
## 2025-03-22 22:11:59.986822 INFO::Fitting model to feature number 263, PWY.6113..superpathway.of.mycolate.biosynthesis
## 2025-03-22 22:11:59.989098 INFO::Fitting model to feature number 264, PWY.5897..superpathway.of.menaquinol.11.biosynthesis
## 2025-03-22 22:11:59.991359 INFO::Fitting model to feature number 265, PWY.5898..superpathway.of.menaquinol.12.biosynthesis
## 2025-03-22 22:11:59.993668 INFO::Fitting model to feature number 266, PWY.5899..superpathway.of.menaquinol.13.biosynthesis
## 2025-03-22 22:11:59.995947 INFO::Fitting model to feature number 267, PWY.7117..C4.photosynthetic.carbon.assimilation.cycle..PEPCK.type
## 2025-03-22 22:11:59.998227 INFO::Fitting model to feature number 268, PWY.6969..TCA.cycle.V..2.oxoglutarate.ferredoxin.oxidoreductase.
## 2025-03-22 22:12:00.000508 INFO::Fitting model to feature number 269, PWY.6628..superpathway.of.L.phenylalanine.biosynthesis
## 2025-03-22 22:12:00.002778 INFO::Fitting model to feature number 270, PWY.5861..superpathway.of.demethylmenaquinol.8.biosynthesis
## 2025-03-22 22:12:00.006207 INFO::Fitting model to feature number 271, PWY.5862..superpathway.of.demethylmenaquinol.9.biosynthesis
## 2025-03-22 22:12:00.008541 INFO::Fitting model to feature number 272, FERMENTATION.PWY..mixed.acid.fermentation
## 2025-03-22 22:12:00.011942 INFO::Fitting model to feature number 273, PWY.241..C4.photosynthetic.carbon.assimilation.cycle..NADP.ME.type
## 2025-03-22 22:12:00.016762 INFO::Fitting model to feature number 274, SO4ASSIM.PWY..sulfate.reduction.I..assimilatory.
## 2025-03-22 22:12:00.019838 INFO::Fitting model to feature number 275, KETOGLUCONMET.PWY..ketogluconate.metabolism
## 2025-03-22 22:12:00.022908 INFO::Fitting model to feature number 276, PWY.5840..superpathway.of.menaquinol.7.biosynthesis
## 2025-03-22 22:12:00.025896 INFO::Fitting model to feature number 277, PWY.5850..superpathway.of.menaquinol.6.biosynthesis.I
## 2025-03-22 22:12:00.029184 INFO::Fitting model to feature number 278, PWY.5896..superpathway.of.menaquinol.10.biosynthesis
## 2025-03-22 22:12:00.031543 INFO::Fitting model to feature number 279, P105.PWY..TCA.cycle.IV..2.oxoglutarate.decarboxylase.
## 2025-03-22 22:12:00.033852 INFO::Fitting model to feature number 280, PWY.5913..TCA.cycle.VI..obligate.autotrophs.
## 2025-03-22 22:12:00.03615 INFO::Fitting model to feature number 281, PWY.561..superpathway.of.glyoxylate.cycle.and.fatty.acid.degradation
## 2025-03-22 22:12:00.038444 INFO::Fitting model to feature number 282, PWY.4702..phytate.degradation.I
## 2025-03-22 22:12:00.04077 INFO::Fitting model to feature number 283, PWY.6803..phosphatidylcholine.acyl.editing
## 2025-03-22 22:12:00.04309 INFO::Fitting model to feature number 284, PWY.7115..C4.photosynthetic.carbon.assimilation.cycle..NAD.ME.type
## 2025-03-22 22:12:00.045398 INFO::Fitting model to feature number 285, PWY.5918..superpathay.of.heme.biosynthesis.from.glutamate
## 2025-03-22 22:12:00.047745 INFO::Fitting model to feature number 286, PWY.7234..inosine.5..phosphate.biosynthesis.III
## 2025-03-22 22:12:00.050971 INFO::Fitting model to feature number 287, PWY.6285..superpathway.of.fatty.acids.biosynthesis..E..coli.
## 2025-03-22 22:12:00.053262 INFO::Fitting model to feature number 288, PWY.5860..superpathway.of.demethylmenaquinol.6.biosynthesis.I
## 2025-03-22 22:12:00.055571 INFO::Fitting model to feature number 289, PWY.5863..superpathway.of.phylloquinol.biosynthesis
## 2025-03-22 22:12:00.057865 INFO::Fitting model to feature number 290, HEME.BIOSYNTHESIS.II..heme.biosynthesis.I..aerobic.
## 2025-03-22 22:12:00.060131 INFO::Fitting model to feature number 291, PWY.821..superpathway.of.sulfur.amino.acid.biosynthesis..Saccharomyces.cerevisiae.
## 2025-03-22 22:12:00.062419 INFO::Fitting model to feature number 292, PWY.5675..nitrate.reduction.V..assimilatory.
## 2025-03-22 22:12:00.064714 INFO::Fitting model to feature number 293, PWY.5791..1.4.dihydroxy.2.naphthoate.biosynthesis.II..plants.
## 2025-03-22 22:12:00.066983 INFO::Fitting model to feature number 294, PWY.5837..1.4.dihydroxy.2.naphthoate.biosynthesis.I
## 2025-03-22 22:12:00.06925 INFO::Fitting model to feature number 295, PWY.5920..superpathway.of.heme.biosynthesis.from.glycine
## 2025-03-22 22:12:00.072553 INFO::Fitting model to feature number 296, PWY.7204..pyridoxal.5..phosphate.salvage.II..plants.
## 2025-03-22 22:12:00.074836 INFO::Fitting model to feature number 297, ENTBACSYN.PWY..enterobactin.biosynthesis
## 2025-03-22 22:12:00.077126 INFO::Fitting model to feature number 298, PWY0.1415..superpathway.of.heme.biosynthesis.from.uroporphyrinogen.III
## 2025-03-22 22:12:00.079444 INFO::Fitting model to feature number 299, HEMESYN2.PWY..heme.biosynthesis.II..anaerobic.
## 2025-03-22 22:12:00.081764 INFO::Fitting model to feature number 300, PWY.6284..superpathway.of.unsaturated.fatty.acids.biosynthesis..E..coli.
## 2025-03-22 22:12:00.084024 INFO::Fitting model to feature number 301, P42.PWY..incomplete.reductive.TCA.cycle
## 2025-03-22 22:12:00.0863 INFO::Fitting model to feature number 302, PWY.5656..mannosylglycerate.biosynthesis.I
## 2025-03-22 22:12:00.08864 INFO::Fitting model to feature number 303, PWY.5173..superpathway.of.acetyl.CoA.biosynthesis
## 2025-03-22 22:12:00.090909 INFO::Fitting model to feature number 304, ECASYN.PWY..enterobacterial.common.antigen.biosynthesis
## 2025-03-22 22:12:00.094083 INFO::Fitting model to feature number 305, AST.PWY..L.arginine.degradation.II..AST.pathway.
## 2025-03-22 22:12:00.096361 INFO::Fitting model to feature number 306, PWY3O.355..stearate.biosynthesis.III..fungi.
## 2025-03-22 22:12:00.098675 INFO::Fitting model to feature number 307, PWY0.42..2.methylcitrate.cycle.I
## 2025-03-22 22:12:00.100934 INFO::Fitting model to feature number 308, PWY.7094..fatty.acid.salvage
## 2025-03-22 22:12:00.103227 INFO::Fitting model to feature number 309, PWY.5747..2.methylcitrate.cycle.II
## 2025-03-22 22:12:00.105558 INFO::Fitting model to feature number 310, PWY.5367..petroselinate.biosynthesis
## 2025-03-22 22:12:00.107866 INFO::Fitting model to feature number 311, PWY0.1533..methylphosphonate.degradation.I
## 2025-03-22 22:12:00.110124 INFO::Fitting model to feature number 312, PWY.6823..molybdenum.cofactor.biosynthesis
## 2025-03-22 22:12:00.112418 INFO::Fitting model to feature number 313, PWY.5705..allantoin.degradation.to.glyoxylate.III
## 2025-03-22 22:12:00.115107 INFO::Fitting model to feature number 314, LPSSYN.PWY..superpathway.of.lipopolysaccharide.biosynthesis
## 2025-03-22 22:12:00.119576 INFO::Fitting model to feature number 315, REDCITCYC..TCA.cycle.VIII..helicobacter.
## 2025-03-22 22:12:00.121851 INFO::Fitting model to feature number 316, GLYCOL.GLYOXDEG.PWY..superpathway.of.glycol.metabolism.and.degradation
## 2025-03-22 22:12:00.124135 INFO::Fitting model to feature number 317, P122.PWY..heterolactic.fermentation
## 2025-03-22 22:12:00.126453 INFO::Fitting model to feature number 318, KDO.NAGLIPASYN.PWY..superpathway.of..Kdo.2.lipid.A.biosynthesis
## 2025-03-22 22:12:00.12875 INFO::Fitting model to feature number 319, PWY.7446..sulfoglycolysis
## 2025-03-22 22:12:00.131006 INFO::Fitting model to feature number 320, PWY490.3..nitrate.reduction.VI..assimilatory.
## 2025-03-22 22:12:00.133303 INFO::Fitting model to feature number 321, PWY.7209..superpathway.of.pyrimidine.ribonucleosides.degradation
## 2025-03-22 22:12:00.135598 INFO::Fitting model to feature number 322, UBISYN.PWY..superpathway.of.ubiquinol.8.biosynthesis..prokaryotic.
## 2025-03-22 22:12:00.138836 INFO::Fitting model to feature number 323, PWY0.41..allantoin.degradation.IV..anaerobic.
## 2025-03-22 22:12:00.141124 INFO::Fitting model to feature number 324, PWY.5855..ubiquinol.7.biosynthesis..prokaryotic.
## 2025-03-22 22:12:00.143382 INFO::Fitting model to feature number 325, PWY.5856..ubiquinol.9.biosynthesis..prokaryotic.
## 2025-03-22 22:12:00.145675 INFO::Fitting model to feature number 326, PWY.5857..ubiquinol.10.biosynthesis..prokaryotic.
## 2025-03-22 22:12:00.147966 INFO::Fitting model to feature number 327, PWY.6708..ubiquinol.8.biosynthesis..prokaryotic.
## 2025-03-22 22:12:00.150238 INFO::Fitting model to feature number 328, PWY.5692..allantoin.degradation.to.glyoxylate.II
## 2025-03-22 22:12:00.152511 INFO::Fitting model to feature number 329, URDEGR.PWY..superpathway.of.allantoin.degradation.in.plants
## 2025-03-22 22:12:00.15478 INFO::Fitting model to feature number 330, PWY0.1338..polymyxin.resistance
## 2025-03-22 22:12:00.1571 INFO::Fitting model to feature number 331, P221.PWY..octane.oxidation
## 2025-03-22 22:12:00.160294 INFO::Fitting model to feature number 332, THREOCAT.PWY..superpathway.of.L.threonine.metabolism
## 2025-03-22 22:12:00.162579 INFO::Fitting model to feature number 333, NONMEVIPP.PWY..methylerythritol.phosphate.pathway.I
## 2025-03-22 22:12:00.16488 INFO::Fitting model to feature number 334, PWY.7560..methylerythritol.phosphate.pathway.II
## 2025-03-22 22:12:00.167174 INFO::Fitting model to feature number 335, PWY.5121..superpathway.of.geranylgeranyl.diphosphate.biosynthesis.II..via.MEP.
## 2025-03-22 22:12:00.169441 INFO::Fitting model to feature number 336, PWY.7392..taxadiene.biosynthesis..engineered.
## 2025-03-22 22:12:00.171726 INFO::Fitting model to feature number 337, PWY.6143..CMP.pseudaminate.biosynthesis
## 2025-03-22 22:12:00.173995 INFO::Fitting model to feature number 338, PWY.6270..isoprene.biosynthesis.I
## 2025-03-22 22:12:00.176258 INFO::Fitting model to feature number 339, ALLANTOINDEG.PWY..superpathway.of.allantoin.degradation.in.yeast
## 2025-03-22 22:12:00.178611 INFO::Fitting model to feature number 340, PWY.6263..superpathway.of.menaquinol.8.biosynthesis.II
## 2025-03-22 22:12:00.181553 INFO::Fitting model to feature number 341, PWY.7371..1.4.dihydroxy.6.naphthoate.biosynthesis.II
## 2025-03-22 22:12:00.184201 INFO::Fitting model to feature number 342, ARGORNPROST.PWY..arginine..ornithine.and.proline.interconversion
## 2025-03-22 22:12:00.186513 INFO::Fitting model to feature number 343, PWY66.398..TCA.cycle.III..animals.
## 2025-03-22 22:12:00.188784 INFO::Fitting model to feature number 344, PWY.5464..superpathway.of.cytosolic.glycolysis..plants...pyruvate.dehydrogenase.and.TCA.cycle
## 2025-03-22 22:12:00.191073 INFO::Fitting model to feature number 345, ORNDEG.PWY..superpathway.of.ornithine.degradation
## 2025-03-22 22:12:00.193343 INFO::Fitting model to feature number 346, P23.PWY..reductive.TCA.cycle.I
## 2025-03-22 22:12:00.195611 INFO::Fitting model to feature number 347, PWY0.1277..3.phenylpropanoate.and.3..3.hydroxyphenyl.propanoate.degradation
## 2025-03-22 22:12:00.197926 INFO::Fitting model to feature number 348, ARGDEG.PWY..superpathway.of.L.arginine..putrescine..and.4.aminobutanoate.degradation
## 2025-03-22 22:12:00.20025 INFO::Fitting model to feature number 349, ORNARGDEG.PWY..superpathway.of.L.arginine.and.L.ornithine.degradation
## 2025-03-22 22:12:00.202559 INFO::Fitting model to feature number 350, HCAMHPDEG.PWY..3.phenylpropanoate.and.3..3.hydroxyphenyl.propanoate.degradation.to.2.oxopent.4.enoate
## 2025-03-22 22:12:00.205739 INFO::Fitting model to feature number 351, PWY.6690..cinnamate.and.3.hydroxycinnamate.degradation.to.2.oxopent.4.enoate
## 2025-03-22 22:12:00.208005 INFO::Fitting model to feature number 352, PROTOCATECHUATE.ORTHO.CLEAVAGE.PWY..protocatechuate.degradation.II..ortho.cleavage.pathway.
## 2025-03-22 22:12:00.210256 INFO::Fitting model to feature number 353, P124.PWY..Bifidobacterium.shunt
## 2025-03-22 22:12:00.212567 INFO::Fitting model to feature number 354, PWY.622..starch.biosynthesis
## 2025-03-22 22:12:00.214848 INFO::Fitting model to feature number 355, PWY.7269..NAD.NADP.NADH.NADPH.mitochondrial.interconversion..yeast.
## 2025-03-22 22:12:00.217133 INFO::Fitting model to feature number 356, PWY.7316..dTDP.N.acetylviosamine.biosynthesis
## 2025-03-22 22:12:00.219779 INFO::Fitting model to feature number 357, PWY.7279..aerobic.respiration.II..cytochrome.c...yeast.
## 2025-03-22 22:12:00.223048 INFO::Fitting model to feature number 358, PWY.6837..fatty.acid.beta.oxidation.V..unsaturated..odd.number..di.isomerase.dependent.
## 2025-03-22 22:12:00.225543 INFO::Fitting model to feature number 359, X3.HYDROXYPHENYLACETATE.DEGRADATION.PWY..4.hydroxyphenylacetate.degradation
## 2025-03-22 22:12:00.228673 INFO::Fitting model to feature number 360, PWY.6953..dTDP.3.acetamido.3.6.dideoxy..alpha..D.galactose.biosynthesis
## 2025-03-22 22:12:00.230936 INFO::Fitting model to feature number 361, PWY.7616..methanol.oxidation.to.carbon.dioxide
## 2025-03-22 22:12:00.2332 INFO::Fitting model to feature number 362, PWY.5088..L.glutamate.degradation.VIII..to.propanoate.
## 2025-03-22 22:12:00.235453 INFO::Fitting model to feature number 363, PWY0.881..superpathway.of.fatty.acid.biosynthesis.I..E..coli.
## 2025-03-22 22:12:00.286126 INFO::Counting total values for each feature
## 2025-03-22 22:12:00.317573 INFO::Writing filtered data to file output_pwys/features/filtered_data.tsv
## 2025-03-22 22:12:00.347011 INFO::Writing filtered, normalized data to file output_pwys/features/filtered_data_norm.tsv
## 2025-03-22 22:12:00.374821 INFO::Writing filtered, normalized, transformed data to file output_pwys/features/filtered_data_norm_transformed.tsv
## 2025-03-22 22:12:00.411565 INFO::Writing residuals to file output_pwys/fits/residuals.rds
## 2025-03-22 22:12:00.434886 INFO::Writing fitted values to file output_pwys/fits/fitted.rds
## 2025-03-22 22:12:00.450001 INFO::Writing all results to file (ordered by increasing q-values): output_pwys/all_results.tsv
## 2025-03-22 22:12:00.454593 INFO::Writing the significant results (those which are less than or equal to the threshold of 0.250000 ) to file (ordered by increasing q-values): output_pwys/significant_results.tsv
## 2025-03-22 22:12:00.455337 INFO::Writing heatmap of significant results to file: output_pwys/heatmap.pdf
## [1] "There are no associations to plot!"
## 2025-03-22 22:12:00.456278 INFO::Writing association plots (one for each significant association) to output folder: output_pwys
## 2025-03-22 22:12:00.459653 INFO::Plotting associations from most to least significant, grouped by metadata
## 2025-03-22 22:12:00.460203 INFO::Plotting data for metadata number 1, antibiotics_current_use
## 2025-03-22 22:12:00.461237 INFO::Creating boxplot for categorical data, antibiotics_current_use vs POLYAMINSYN3.PWY..superpathway.of.polyamine.biosynthesis.II
##########################
# Extract the residuals #
##########################
datExpr <- as.data.frame(t(fit_data$residuals))
########################
# Create WGCNA modules #
########################
gsg = goodSamplesGenes(datExpr, verbose = 3)
## Flagging genes and samples with too many missing values...
## ..step 1
## ..Excluding 6 samples from the calculation due to too many missing genes.
## ..step 2
gsg$allOK
## [1] FALSE
if (!gsg$allOK)
{if (sum(!gsg$goodGenes) > 0)
printFlush(paste(
"Removing genes:",
paste(names(datExpr)[!gsg$goodGenes], collapse = ", ")));
if (sum(!gsg$goodSamples) > 0)
printFlush(paste(
"Removing samples:",
paste(rownames(datExpr)[!gsg$goodSamples], collapse =", ")))
datExpr = datExpr[gsg$goodSamples, gsg$goodGenes]
}
## Removing samples: CSM5MCVB_P, CSM79HNY_P, ESM5GEYY_P, ESM718U9_P, MSM6J2N6_P, MSM9VZLX_P
gsg = goodSamplesGenes(datExpr, verbose = 3)
## Flagging genes and samples with too many missing values...
## ..step 1
gsg$allOK # TRUE
## [1] TRUE
###################################
# Choose soft threshold parameter #
###################################
powers = c(c(1:20), seq(from = 22, to=30, by=2))
sft = pickSoftThreshold(
datExpr, powerVector = powers, verbose = 5, dataIsExpr = TRUE,
RsquaredCut = 0.30)
## pickSoftThreshold: will use block size 363.
## pickSoftThreshold: calculating connectivity for given powers...
## ..working on genes 1 through 363 of 363
## Power SFT.R.sq slope truncated.R.sq mean.k. median.k. max.k.
## 1 1 0.722 1.8100 0.7110 124.00 130.000 162.00
## 2 2 0.596 0.6920 0.6290 63.10 68.700 95.70
## 3 3 0.393 0.2300 0.2310 38.40 39.700 69.30
## 4 4 0.124 -0.0902 0.0162 25.90 24.800 55.00
## 5 5 0.561 -0.3550 0.5860 18.70 16.300 46.60
## 6 6 0.673 -0.5190 0.6680 14.20 11.400 40.40
## 7 7 0.781 -0.6230 0.8100 11.20 8.380 35.60
## 8 8 0.815 -0.7040 0.8450 9.07 6.520 31.80
## 9 9 0.861 -0.8180 0.9260 7.54 5.100 28.60
## 10 10 0.847 -0.8620 0.9070 6.39 4.100 26.00
## 11 11 0.835 -0.9150 0.9140 5.50 3.430 23.80
## 12 12 0.847 -0.9540 0.9130 4.80 2.870 21.90
## 13 13 0.868 -0.9730 0.9370 4.24 2.380 20.20
## 14 14 0.864 -0.9990 0.9160 3.78 2.060 18.70
## 15 15 0.890 -1.0300 0.9590 3.40 1.720 17.40
## 16 16 0.898 -1.0400 0.9670 3.09 1.530 16.20
## 17 17 0.888 -1.0600 0.9570 2.82 1.370 15.20
## 18 18 0.877 -1.0600 0.9290 2.59 1.280 14.20
## 19 19 0.864 -1.0500 0.9170 2.40 1.180 13.30
## 20 20 0.844 -1.0600 0.8690 2.23 1.100 12.50
## 21 22 0.854 -1.0700 0.8890 1.95 0.997 11.20
## 22 24 0.820 -1.0600 0.8720 1.74 0.899 9.98
## 23 26 0.797 -0.9790 0.8720 1.57 0.793 8.97
## 24 28 0.829 -0.9390 0.8720 1.43 0.718 8.10
## 25 30 0.807 -0.9130 0.8140 1.31 0.673 7.35
##############################
# One-step module detection #
##############################
power = sft$powerEstimate
net = blockwiseModules(
datExpr,
power = power,
corFnc = "bicor",
corOptions = list(maxPOutliers = 0.1),
networkType ="unsigned",
maxBlockSize = ncol(datExpr),
minModuleSize = 3,
TOMType = "unsigned",
reassignThreshold = 0,
mergeCutHeight = 0,
verbose = 3)
## Calculating module eigengenes block-wise from all genes
## Flagging genes and samples with too many missing values...
## ..step 1
## ..Working on block 1 .
## TOM calculation: adjacency..
## ..will not use multithreading.
## Fraction of slow calculations: 0.000000
## ..connectivity..
## ..matrix multiplication (system BLAS)..
## ..normalization..
## ..done.
## ....clustering..
## ....detecting modules..
## ....calculating module eigengenes..
## ....checking kME in modules..
## ..removing 3 genes from module 1 because their KME is too low.
## ..removing 11 genes from module 2 because their KME is too low.
## ..removing 2 genes from module 3 because their KME is too low.
## ..merging modules that are too close..
## mergeCloseModules: Merging modules whose distance is less than 0
## Calculating new MEs...
####################
# How many modules #
####################
ncol(net$MEs)
## [1] 4
table(net$colors)
##
## blue brown grey turquoise
## 139 18 16 190
##########################
# Plot module dendrogram #
##########################
eigenGenes <- net$MEs
MEDiss = 1-cor(eigenGenes)
METree = hclust(as.dist(MEDiss), method = "average")
plot(METree, main = "Clustering of module eigengenes", xlab = "", sub = "")
###########################################
# Re-calculate modules and find hub genes #
###########################################
moduleColors <- net$colors
MEs0 = moduleEigengenes(datExpr, moduleColors)$eigengenes
modules_data = orderMEs(MEs0)
#######################
# Create mapping file #
#######################
feature_by_modules <- as.data.frame(net$colors)
feature_by_modules <- rownames_to_column(feature_by_modules)
colnames(feature_by_modules) <- c('Feature', 'Module')
features_mapping <- feature_by_modules
features_mapping$Module <- paste('ME', features_mapping$Module, sep = '')We perform the MSEA as before using the modules from the WGCNA analysis on the pathways.
###################
# Rank DA results #
###################
results <- fit_data$results |> filter(metadata=='disease')
results$qval <- p.adjust(results$pval, 'BH')
sum(results$qval < 0.05)
## [1] 0
results <- results[order(results$qval, decreasing = FALSE),]
###################
# MSEA Processing #
##################
module_map <- features_mapping
mod.gs <- tapply(module_map$Module, module_map$Feature, as.character)
microbeSet <- inverseList(mod.gs)
microbeSet
## $MEblue
## [1] "ANAEROFRUCAT.PWY..homolactic.fermentation"
## [2] "ANAGLYCOLYSIS.PWY..glycolysis.III..from.glucose."
## [3] "ARGININE.SYN4.PWY..L.ornithine.de.novo..biosynthesis"
## [4] "ARGSYN.PWY..L.arginine.biosynthesis.I..via.L.ornithine."
## [5] "ARGSYNBSUB.PWY..L.arginine.biosynthesis.II..acetyl.cycle."
## [6] "ARO.PWY..chorismate.biosynthesis.I"
## [7] "ASPASN.PWY..superpathway.of.L.aspartate.and.L.asparagine.biosynthesis"
## [8] "BRANCHED.CHAIN.AA.SYN.PWY..superpathway.of.branched.amino.acid.biosynthesis"
## [9] "CALVIN.PWY..Calvin.Benson.Bassham.cycle"
## [10] "CITRULBIO.PWY..L.citrulline.biosynthesis"
## [11] "COA.PWY..coenzyme.A.biosynthesis.I"
## [12] "COA.PWY.1..coenzyme.A.biosynthesis.II..mammalian."
## [13] "COBALSYN.PWY..adenosylcobalamin.salvage.from.cobinamide.I"
## [14] "COLANSYN.PWY..colanic.acid.building.blocks.biosynthesis"
## [15] "COMPLETE.ARO.PWY..superpathway.of.aromatic.amino.acid.biosynthesis"
## [16] "DENOVOPURINE2.PWY..superpathway.of.purine.nucleotides.de.novo.biosynthesis.II"
## [17] "DTDPRHAMSYN.PWY..dTDP.L.rhamnose.biosynthesis.I"
## [18] "GALACT.GLUCUROCAT.PWY..superpathway.of.hexuronide.and.hexuronate.degradation"
## [19] "GALACTUROCAT.PWY..D.galacturonate.degradation.I"
## [20] "GLUCONEO.PWY..gluconeogenesis.I"
## [21] "GLUCUROCAT.PWY..superpathway.of..beta..D.glucuronide.and.D.glucuronate.degradation"
## [22] "GLUTORN.PWY..L.ornithine.biosynthesis"
## [23] "GLYCOGENSYNTH.PWY..glycogen.biosynthesis.I..from.ADP.D.Glucose."
## [24] "GLYCOLYSIS..glycolysis.I..from.glucose.6.phosphate."
## [25] "HISDEG.PWY..L.histidine.degradation.I"
## [26] "HISTSYN.PWY..L.histidine.biosynthesis"
## [27] "HSERMETANA.PWY..L.methionine.biosynthesis.III"
## [28] "ILEUSYN.PWY..L.isoleucine.biosynthesis.I..from.threonine."
## [29] "NAGLIPASYN.PWY..lipid.IVA.biosynthesis"
## [30] "NONOXIPENT.PWY..pentose.phosphate.pathway..non.oxidative.branch."
## [31] "OANTIGEN.PWY..O.antigen.building.blocks.biosynthesis..E..coli."
## [32] "P108.PWY..pyruvate.fermentation.to.propanoate.I"
## [33] "PANTO.PWY..phosphopantothenate.biosynthesis.I"
## [34] "PANTOSYN.PWY..pantothenate.and.coenzyme.A.biosynthesis.I"
## [35] "PENTOSE.P.PWY..pentose.phosphate.pathway"
## [36] "PEPTIDOGLYCANSYN.PWY..peptidoglycan.biosynthesis.I..meso.diaminopimelate.containing."
## [37] "PHOSLIPSYN.PWY..superpathway.of.phospholipid.biosynthesis.I..bacteria."
## [38] "POLYISOPRENSYN.PWY..polyisoprenoid.biosynthesis..E..coli."
## [39] "PWY.1042..glycolysis.IV..plant.cytosol."
## [40] "PWY.1269..CMP.3.deoxy.D.manno.octulosonate.biosynthesis.I"
## [41] "PWY.2941..L.lysine.biosynthesis.II"
## [42] "PWY.2942..L.lysine.biosynthesis.III"
## [43] "PWY.3001..superpathway.of.L.isoleucine.biosynthesis.I"
## [44] "PWY.3841..folate.transformations.II"
## [45] "PWY.4242..pantothenate.and.coenzyme.A.biosynthesis.III"
## [46] "PWY.4981..L.proline.biosynthesis.II..from.arginine."
## [47] "PWY.4984..urea.cycle"
## [48] "PWY.5030..L.histidine.degradation.III"
## [49] "PWY.5097..L.lysine.biosynthesis.VI"
## [50] "PWY.5103..L.isoleucine.biosynthesis.III"
## [51] "PWY.5154..L.arginine.biosynthesis.III..via.N.acetyl.L.citrulline."
## [52] "PWY.5304..superpathway.of.sulfur.oxidation..Acidianus.ambivalens."
## [53] "PWY.5484..glycolysis.II..from.fructose.6.phosphate."
## [54] "PWY.5505..L.glutamate.and.L.glutamine.biosynthesis"
## [55] "PWY.5659..GDP.mannose.biosynthesis"
## [56] "PWY.5667..CDP.diacylglycerol.biosynthesis.I"
## [57] "PWY.5686..UMP.biosynthesis"
## [58] "PWY.5695..urate.biosynthesis.inosine.5..phosphate.degradation"
## [59] "PWY.5941..glycogen.degradation.II..eukaryotic."
## [60] "PWY.5973..cis.vaccenate.biosynthesis"
## [61] "PWY.6121..5.aminoimidazole.ribonucleotide.biosynthesis.I"
## [62] "PWY.6122..5.aminoimidazole.ribonucleotide.biosynthesis.II"
## [63] "PWY.6123..inosine.5..phosphate.biosynthesis.I"
## [64] "PWY.6124..inosine.5..phosphate.biosynthesis.II"
## [65] "PWY.6125..superpathway.of.guanosine.nucleotides.de.novo.biosynthesis.II"
## [66] "PWY.6126..superpathway.of.adenosine.nucleotides.de.novo.biosynthesis.II"
## [67] "PWY.6147..6.hydroxymethyl.dihydropterin.diphosphate.biosynthesis.I"
## [68] "PWY.6151..S.adenosyl.L.methionine.cycle.I"
## [69] "PWY.6163..chorismate.biosynthesis.from.3.dehydroquinate"
## [70] "PWY.6168..flavin.biosynthesis.III..fungi."
## [71] "PWY.621..sucrose.degradation.III..sucrose.invertase."
## [72] "PWY.6277..superpathway.of.5.aminoimidazole.ribonucleotide.biosynthesis"
## [73] "PWY.6305..putrescine.biosynthesis.IV"
## [74] "PWY.6317..galactose.degradation.I..Leloir.pathway."
## [75] "PWY.6385..peptidoglycan.biosynthesis.III..mycobacteria."
## [76] "PWY.6386..UDP.N.acetylmuramoyl.pentapeptide.biosynthesis.II..lysine.containing."
## [77] "PWY.6387..UDP.N.acetylmuramoyl.pentapeptide.biosynthesis.I..meso.diaminopimelate.containing."
## [78] "PWY.6507..4.deoxy.L.threo.hex.4.enopyranuronate.degradation"
## [79] "PWY.6545..pyrimidine.deoxyribonucleotides.de.novo.biosynthesis.III"
## [80] "PWY.6572..chondroitin.sulfate.degradation.I..bacterial."
## [81] "PWY.6609..adenine.and.adenosine.salvage.III"
## [82] "PWY.6700..queuosine.biosynthesis"
## [83] "PWY.6703..preQ0.biosynthesis"
## [84] "PWY.6737..starch.degradation.V"
## [85] "PWY.6859..all.trans.farnesol.biosynthesis"
## [86] "PWY.6892..thiazole.biosynthesis.I..E..coli."
## [87] "PWY.6897..thiamin.salvage.II"
## [88] "PWY.6901..superpathway.of.glucose.and.xylose.degradation"
## [89] "PWY.6936..seleno.amino.acid.biosynthesis"
## [90] "PWY.7111..pyruvate.fermentation.to.isobutanol..engineered."
## [91] "PWY.7184..pyrimidine.deoxyribonucleotides.de.novo.biosynthesis.I"
## [92] "PWY.7187..pyrimidine.deoxyribonucleotides.de.novo.biosynthesis.II"
## [93] "PWY.7197..pyrimidine.deoxyribonucleotide.phosphorylation"
## [94] "PWY.7199..pyrimidine.deoxyribonucleosides.salvage"
## [95] "PWY.7208..superpathway.of.pyrimidine.nucleobases.salvage"
## [96] "PWY.7210..pyrimidine.deoxyribonucleotides.biosynthesis.from.CTP"
## [97] "PWY.7211..superpathway.of.pyrimidine.deoxyribonucleotides.de.novo.biosynthesis"
## [98] "PWY.7219..adenosine.ribonucleotides.de.novo.biosynthesis"
## [99] "PWY.7220..adenosine.deoxyribonucleotides.de.novo.biosynthesis.II"
## [100] "PWY.7221..guanosine.ribonucleotides.de.novo.biosynthesis"
## [101] "PWY.7222..guanosine.deoxyribonucleotides.de.novo.biosynthesis.II"
## [102] "PWY.7228..superpathway.of.guanosine.nucleotides.de.novo.biosynthesis.I"
## [103] "PWY.7229..superpathway.of.adenosine.nucleotides.de.novo.biosynthesis.I"
## [104] "PWY.7234..inosine.5..phosphate.biosynthesis.III"
## [105] "PWY.724..superpathway.of.L.lysine..L.threonine.and.L.methionine.biosynthesis.II"
## [106] "PWY.7242..D.fructuronate.degradation"
## [107] "PWY.7282..4.amino.2.methyl.5.phosphomethylpyrimidine.biosynthesis..yeast."
## [108] "PWY.7323..superpathway.of.GDP.mannose.derived.O.antigen.building.blocks.biosynthesis"
## [109] "PWY.7332..superpathway.of.UDP.N.acetylglucosamine.derived.O.antigen.building.blocks.biosynthesis"
## [110] "PWY.7357..thiamin.formation.from.pyrithiamine.and.oxythiamine..yeast."
## [111] "PWY.7383..anaerobic.energy.metabolism..invertebrates..cytosol."
## [112] "PWY.7400..L.arginine.biosynthesis.IV..archaebacteria."
## [113] "PWY.7456..mannan.degradation"
## [114] "PWY.7539..6.hydroxymethyl.dihydropterin.diphosphate.biosynthesis.III..Chlamydia."
## [115] "PWY.7663..gondoate.biosynthesis..anaerobic."
## [116] "PWY.841..superpathway.of.purine.nucleotides.de.novo.biosynthesis.I"
## [117] "PWY0.1296..purine.ribonucleosides.degradation"
## [118] "PWY0.1319..CDP.diacylglycerol.biosynthesis.II"
## [119] "PWY0.1586..peptidoglycan.maturation..meso.diaminopimelate.containing."
## [120] "PWY0.162..superpathway.of.pyrimidine.ribonucleotides.de.novo.biosynthesis"
## [121] "PWY0.166..superpathway.of.pyrimidine.deoxyribonucleotides.de.novo.biosynthesis..E..coli."
## [122] "PWY0.845..superpathway.of.pyridoxal.5..phosphate.biosynthesis.and.salvage"
## [123] "PWY4FS.7..phosphatidylglycerol.biosynthesis.I..plastidic."
## [124] "PWY4FS.8..phosphatidylglycerol.biosynthesis.II..non.plastidic."
## [125] "PWY66.399..gluconeogenesis.III"
## [126] "PWY66.422..D.galactose.degradation.V..Leloir.pathway."
## [127] "PYRIDNUCSYN.PWY..NAD.biosynthesis.I..from.aspartate."
## [128] "PYRIDOXSYN.PWY..pyridoxal.5..phosphate.biosynthesis.I"
## [129] "RHAMCAT.PWY..L.rhamnose.degradation.I"
## [130] "RIBOSYN2.PWY..flavin.biosynthesis.I..bacteria.and.plants."
## [131] "SER.GLYSYN.PWY..superpathway.of.L.serine.and.glycine.biosynthesis.I"
## [132] "TEICHOICACID.PWY..teichoic.acid..poly.glycerol..biosynthesis"
## [133] "THISYN.PWY..superpathway.of.thiamin.diphosphate.biosynthesis.I"
## [134] "THISYNARA.PWY..superpathway.of.thiamin.diphosphate.biosynthesis.III..eukaryotes."
## [135] "THRESYN.PWY..superpathway.of.L.threonine.biosynthesis"
## [136] "TRNA.CHARGING.PWY..tRNA.charging"
## [137] "TRPSYN.PWY..L.tryptophan.biosynthesis"
## [138] "VALSYN.PWY..L.valine.biosynthesis"
## [139] "X1CMET2.PWY..N10.formyl.tetrahydrofolate.biosynthesis"
##
## $MEbrown
## [1] "GLCMANNANAUT.PWY..superpathway.of.N.acetylglucosamine..N.acetylmannosamine.and.N.acetylneuraminate.degradation"
## [2] "GLYCOLYSIS.E.D..superpathway.of.glycolysis.and.Entner.Doudoroff"
## [3] "METH.ACETATE.PWY..methanogenesis.from.acetate"
## [4] "PWY.5100..pyruvate.fermentation.to.acetate.and.lactate.II"
## [5] "PWY.5104..L.isoleucine.biosynthesis.IV"
## [6] "PWY.5177..glutaryl.CoA.degradation"
## [7] "PWY.5690..TCA.cycle.II..plants.and.fungi."
## [8] "PWY.6470..peptidoglycan.biosynthesis.V...beta..lactam.resistance."
## [9] "PWY.6527..stachyose.degradation"
## [10] "PWY.6595..superpathway.of.guanosine.nucleotides.degradation..plants."
## [11] "PWY.6608..guanosine.nucleotides.degradation.III"
## [12] "PWY.7196..superpathway.of.pyrimidine.ribonucleosides.salvage"
## [13] "PWY.7198..pyrimidine.deoxyribonucleotides.de.novo.biosynthesis.IV"
## [14] "PWY0.1061..superpathway.of.L.alanine.biosynthesis"
## [15] "PWY0.1261..anhydromuropeptides.recycling"
## [16] "PWY66.400..glycolysis.VI..metazoan."
## [17] "TCA..TCA.cycle.I..prokaryotic."
## [18] "UDPNAGSYN.PWY..UDP.N.acetyl.D.glucosamine.biosynthesis.I"
##
## $MEgrey
## [1] "NAD.BIOSYNTHESIS.II..NAD.salvage.pathway.II"
## [2] "P162.PWY..L.glutamate.degradation.V..via.hydroxyglutarate."
## [3] "P163.PWY..L.lysine.fermentation.to.acetate.and.butanoate"
## [4] "PWY.3781..aerobic.respiration.I..cytochrome.c."
## [5] "PWY.6143..CMP.pseudaminate.biosynthesis"
## [6] "PWY.622..starch.biosynthesis"
## [7] "PWY.6263..superpathway.of.menaquinol.8.biosynthesis.II"
## [8] "PWY.6478..GDP.D.glycero..alpha..D.manno.heptose.biosynthesis"
## [9] "PWY.6749..CMP.legionaminate.biosynthesis.I"
## [10] "PWY.6953..dTDP.3.acetamido.3.6.dideoxy..alpha..D.galactose.biosynthesis"
## [11] "PWY.7237..myo...chiro..and.scillo.inositol.degradation"
## [12] "PWY.7312..dTDP.D..beta..fucofuranose.biosynthesis"
## [13] "PWY.7316..dTDP.N.acetylviosamine.biosynthesis"
## [14] "PWY.7371..1.4.dihydroxy.6.naphthoate.biosynthesis.II"
## [15] "PWY490.3..nitrate.reduction.VI..assimilatory."
## [16] "RUMP.PWY..formaldehyde.oxidation.I"
##
## $MEturquoise
## [1] "ALLANTOINDEG.PWY..superpathway.of.allantoin.degradation.in.yeast"
## [2] "ARG.POLYAMINE.SYN..superpathway.of.arginine.and.polyamine.biosynthesis"
## [3] "ARGDEG.PWY..superpathway.of.L.arginine..putrescine..and.4.aminobutanoate.degradation"
## [4] "ARGORNPROST.PWY..arginine..ornithine.and.proline.interconversion"
## [5] "AST.PWY..L.arginine.degradation.II..AST.pathway."
## [6] "BIOTIN.BIOSYNTHESIS.PWY..biotin.biosynthesis.I"
## [7] "CENTFERM.PWY..pyruvate.fermentation.to.butanoate"
## [8] "DAPLYSINESYN.PWY..L.lysine.biosynthesis.I"
## [9] "ECASYN.PWY..enterobacterial.common.antigen.biosynthesis"
## [10] "ENTBACSYN.PWY..enterobactin.biosynthesis"
## [11] "FAO.PWY..fatty.acid..beta..oxidation.I"
## [12] "FASYN.ELONG.PWY..fatty.acid.elongation....saturated"
## [13] "FASYN.INITIAL.PWY..superpathway.of.fatty.acid.biosynthesis.initiation..E..coli."
## [14] "FERMENTATION.PWY..mixed.acid.fermentation"
## [15] "FOLSYN.PWY..superpathway.of.tetrahydrofolate.biosynthesis.and.salvage"
## [16] "FUC.RHAMCAT.PWY..superpathway.of.fucose.and.rhamnose.degradation"
## [17] "FUCCAT.PWY..fucose.degradation"
## [18] "GALACTARDEG.PWY..D.galactarate.degradation.I"
## [19] "GLUCARDEG.PWY..D.glucarate.degradation.I"
## [20] "GLUCARGALACTSUPER.PWY..superpathway.of.D.glucarate.and.D.galactarate.degradation"
## [21] "GLUCOSE1PMETAB.PWY..glucose.and.glucose.1.phosphate.degradation"
## [22] "GLUDEG.I.PWY..GABA.shunt"
## [23] "GLYCOCAT.PWY..glycogen.degradation.I..bacterial."
## [24] "GLYCOL.GLYOXDEG.PWY..superpathway.of.glycol.metabolism.and.degradation"
## [25] "GLYCOLYSIS.TCA.GLYOX.BYPASS..superpathway.of.glycolysis..pyruvate.dehydrogenase..TCA..and.glyoxylate.bypass"
## [26] "GLYOXYLATE.BYPASS..glyoxylate.cycle"
## [27] "GOLPDLCAT.PWY..superpathway.of.glycerol.degradation.to.1.3.propanediol"
## [28] "HCAMHPDEG.PWY..3.phenylpropanoate.and.3..3.hydroxyphenyl.propanoate.degradation.to.2.oxopent.4.enoate"
## [29] "HEME.BIOSYNTHESIS.II..heme.biosynthesis.I..aerobic."
## [30] "HEMESYN2.PWY..heme.biosynthesis.II..anaerobic."
## [31] "HEXITOLDEGSUPER.PWY..superpathway.of.hexitol.degradation..bacteria."
## [32] "HOMOSER.METSYN.PWY..L.methionine.biosynthesis.I"
## [33] "KDO.NAGLIPASYN.PWY..superpathway.of..Kdo.2.lipid.A.biosynthesis"
## [34] "KETOGLUCONMET.PWY..ketogluconate.metabolism"
## [35] "LACTOSECAT.PWY..lactose.and.galactose.degradation.I"
## [36] "LPSSYN.PWY..superpathway.of.lipopolysaccharide.biosynthesis"
## [37] "MET.SAM.PWY..superpathway.of.S.adenosyl.L.methionine.biosynthesis"
## [38] "METHGLYUT.PWY..superpathway.of.methylglyoxal.degradation"
## [39] "METSYN.PWY..L.homoserine.and.L.methionine.biosynthesis"
## [40] "NONMEVIPP.PWY..methylerythritol.phosphate.pathway.I"
## [41] "ORNARGDEG.PWY..superpathway.of.L.arginine.and.L.ornithine.degradation"
## [42] "ORNDEG.PWY..superpathway.of.ornithine.degradation"
## [43] "P105.PWY..TCA.cycle.IV..2.oxoglutarate.decarboxylase."
## [44] "P122.PWY..heterolactic.fermentation"
## [45] "P124.PWY..Bifidobacterium.shunt"
## [46] "P161.PWY..acetylene.degradation"
## [47] "P164.PWY..purine.nucleobases.degradation.I..anaerobic."
## [48] "P185.PWY..formaldehyde.assimilation.III..dihydroxyacetone.cycle."
## [49] "P221.PWY..octane.oxidation"
## [50] "P23.PWY..reductive.TCA.cycle.I"
## [51] "P4.PWY..superpathway.of.L.lysine..L.threonine.and.L.methionine.biosynthesis.I"
## [52] "P42.PWY..incomplete.reductive.TCA.cycle"
## [53] "P441.PWY..superpathway.of.N.acetylneuraminate.degradation"
## [54] "P461.PWY..hexitol.fermentation.to.lactate..formate..ethanol.and.acetate"
## [55] "POLYAMINSYN3.PWY..superpathway.of.polyamine.biosynthesis.II"
## [56] "POLYAMSYN.PWY..superpathway.of.polyamine.biosynthesis.I"
## [57] "PPGPPMET.PWY..ppGpp.biosynthesis"
## [58] "PROTOCATECHUATE.ORTHO.CLEAVAGE.PWY..protocatechuate.degradation.II..ortho.cleavage.pathway."
## [59] "PRPP.PWY..superpathway.of.histidine..purine..and.pyrimidine.biosynthesis"
## [60] "PWY.1861..formaldehyde.assimilation.II..RuMP.Cycle."
## [61] "PWY.241..C4.photosynthetic.carbon.assimilation.cycle..NADP.ME.type"
## [62] "PWY.2723..trehalose.degradation.V"
## [63] "PWY.4041...gamma..glutamyl.cycle"
## [64] "PWY.4702..phytate.degradation.I"
## [65] "PWY.5005..biotin.biosynthesis.II"
## [66] "PWY.5022..4.aminobutanoate.degradation.V"
## [67] "PWY.5083..NAD.NADH.phosphorylation.and.dephosphorylation"
## [68] "PWY.5088..L.glutamate.degradation.VIII..to.propanoate."
## [69] "PWY.5121..superpathway.of.geranylgeranyl.diphosphate.biosynthesis.II..via.MEP."
## [70] "PWY.5136..fatty.acid..beta..oxidation.II..peroxisome."
## [71] "PWY.5138..unsaturated..even.numbered.fatty.acid..beta..oxidation"
## [72] "PWY.5173..superpathway.of.acetyl.CoA.biosynthesis"
## [73] "PWY.5188..tetrapyrrole.biosynthesis.I..from.glutamate."
## [74] "PWY.5189..tetrapyrrole.biosynthesis.II..from.glycine."
## [75] "PWY.5345..superpathway.of.L.methionine.biosynthesis..by.sulfhydrylation."
## [76] "PWY.5347..superpathway.of.L.methionine.biosynthesis..transsulfuration."
## [77] "PWY.5367..petroselinate.biosynthesis"
## [78] "PWY.5384..sucrose.degradation.IV..sucrose.phosphorylase."
## [79] "PWY.5464..superpathway.of.cytosolic.glycolysis..plants...pyruvate.dehydrogenase.and.TCA.cycle"
## [80] "PWY.561..superpathway.of.glyoxylate.cycle.and.fatty.acid.degradation"
## [81] "PWY.5656..mannosylglycerate.biosynthesis.I"
## [82] "PWY.5675..nitrate.reduction.V..assimilatory."
## [83] "PWY.5676..acetyl.CoA.fermentation.to.butanoate.II"
## [84] "PWY.5677..succinate.fermentation.to.butanoate"
## [85] "PWY.5692..allantoin.degradation.to.glyoxylate.II"
## [86] "PWY.5705..allantoin.degradation.to.glyoxylate.III"
## [87] "PWY.5723..Rubisco.shunt"
## [88] "PWY.5747..2.methylcitrate.cycle.II"
## [89] "PWY.5791..1.4.dihydroxy.2.naphthoate.biosynthesis.II..plants."
## [90] "PWY.5837..1.4.dihydroxy.2.naphthoate.biosynthesis.I"
## [91] "PWY.5838..superpathway.of.menaquinol.8.biosynthesis.I"
## [92] "PWY.5840..superpathway.of.menaquinol.7.biosynthesis"
## [93] "PWY.5845..superpathway.of.menaquinol.9.biosynthesis"
## [94] "PWY.5850..superpathway.of.menaquinol.6.biosynthesis.I"
## [95] "PWY.5855..ubiquinol.7.biosynthesis..prokaryotic."
## [96] "PWY.5856..ubiquinol.9.biosynthesis..prokaryotic."
## [97] "PWY.5857..ubiquinol.10.biosynthesis..prokaryotic."
## [98] "PWY.5860..superpathway.of.demethylmenaquinol.6.biosynthesis.I"
## [99] "PWY.5861..superpathway.of.demethylmenaquinol.8.biosynthesis"
## [100] "PWY.5862..superpathway.of.demethylmenaquinol.9.biosynthesis"
## [101] "PWY.5863..superpathway.of.phylloquinol.biosynthesis"
## [102] "PWY.5896..superpathway.of.menaquinol.10.biosynthesis"
## [103] "PWY.5897..superpathway.of.menaquinol.11.biosynthesis"
## [104] "PWY.5898..superpathway.of.menaquinol.12.biosynthesis"
## [105] "PWY.5899..superpathway.of.menaquinol.13.biosynthesis"
## [106] "PWY.5913..TCA.cycle.VI..obligate.autotrophs."
## [107] "PWY.5918..superpathay.of.heme.biosynthesis.from.glutamate"
## [108] "PWY.5920..superpathway.of.heme.biosynthesis.from.glycine"
## [109] "PWY.5971..palmitate.biosynthesis.II..bacteria.and.plants."
## [110] "PWY.5989..stearate.biosynthesis.II..bacteria.and.plants."
## [111] "PWY.6113..superpathway.of.mycolate.biosynthesis"
## [112] "PWY.6270..isoprene.biosynthesis.I"
## [113] "PWY.6282..palmitoleate.biosynthesis.I..from..5Z..dodec.5.enoate."
## [114] "PWY.6284..superpathway.of.unsaturated.fatty.acids.biosynthesis..E..coli."
## [115] "PWY.6285..superpathway.of.fatty.acids.biosynthesis..E..coli."
## [116] "PWY.6318..L.phenylalanine.degradation.IV..mammalian..via.side.chain."
## [117] "PWY.6353..purine.nucleotides.degradation.II..aerobic."
## [118] "PWY.6471..peptidoglycan.biosynthesis.IV..Enterococcus.faecium."
## [119] "PWY.6519..8.amino.7.oxononanoate.biosynthesis.I"
## [120] "PWY.6531..mannitol.cycle"
## [121] "PWY.6549..L.glutamine.biosynthesis.III"
## [122] "PWY.6588..pyruvate.fermentation.to.acetone"
## [123] "PWY.6590..superpathway.of.Clostridium.acetobutylicum.acidogenic.fermentation"
## [124] "PWY.6606..guanosine.nucleotides.degradation.II"
## [125] "PWY.6612..superpathway.of.tetrahydrofolate.biosynthesis"
## [126] "PWY.6628..superpathway.of.L.phenylalanine.biosynthesis"
## [127] "PWY.6629..superpathway.of.L.tryptophan.biosynthesis"
## [128] "PWY.6630..superpathway.of.L.tyrosine.biosynthesis"
## [129] "PWY.6690..cinnamate.and.3.hydroxycinnamate.degradation.to.2.oxopent.4.enoate"
## [130] "PWY.6708..ubiquinol.8.biosynthesis..prokaryotic."
## [131] "PWY.6731..starch.degradation.III"
## [132] "PWY.6803..phosphatidylcholine.acyl.editing"
## [133] "PWY.6823..molybdenum.cofactor.biosynthesis"
## [134] "PWY.6837..fatty.acid.beta.oxidation.V..unsaturated..odd.number..di.isomerase.dependent."
## [135] "PWY.6876..isopropanol.biosynthesis"
## [136] "PWY.6891..thiazole.biosynthesis.II..Bacillus."
## [137] "PWY.6895..superpathway.of.thiamin.diphosphate.biosynthesis.II"
## [138] "PWY.6969..TCA.cycle.V..2.oxoglutarate.ferredoxin.oxidoreductase."
## [139] "PWY.7003..glycerol.degradation.to.butanol"
## [140] "PWY.7013..L.1.2.propanediol.degradation"
## [141] "PWY.7046..4.coumarate.degradation..anaerobic."
## [142] "PWY.7094..fatty.acid.salvage"
## [143] "PWY.7115..C4.photosynthetic.carbon.assimilation.cycle..NAD.ME.type"
## [144] "PWY.7117..C4.photosynthetic.carbon.assimilation.cycle..PEPCK.type"
## [145] "PWY.7204..pyridoxal.5..phosphate.salvage.II..plants."
## [146] "PWY.7209..superpathway.of.pyrimidine.ribonucleosides.degradation"
## [147] "PWY.7254..TCA.cycle.VII..acetate.producers."
## [148] "PWY.7269..NAD.NADP.NADH.NADPH.mitochondrial.interconversion..yeast."
## [149] "PWY.7279..aerobic.respiration.II..cytochrome.c...yeast."
## [150] "PWY.7288..fatty.acid..beta..oxidation..peroxisome..yeast."
## [151] "PWY.7315..dTDP.N.acetylthomosamine.biosynthesis"
## [152] "PWY.7328..superpathway.of.UDP.glucose.derived.O.antigen.building.blocks.biosynthesis"
## [153] "PWY.7385..1.3.propanediol.biosynthesis..engineered."
## [154] "PWY.7388..octanoyl..acyl.carrier.protein..biosynthesis..mitochondria..yeast."
## [155] "PWY.7392..taxadiene.biosynthesis..engineered."
## [156] "PWY.7446..sulfoglycolysis"
## [157] "PWY.7560..methylerythritol.phosphate.pathway.II"
## [158] "PWY.7616..methanol.oxidation.to.carbon.dioxide"
## [159] "PWY.7664..oleate.biosynthesis.IV..anaerobic."
## [160] "PWY.821..superpathway.of.sulfur.amino.acid.biosynthesis..Saccharomyces.cerevisiae."
## [161] "PWY0.1241..ADP.L.glycero..beta..D.manno.heptose.biosynthesis"
## [162] "PWY0.1277..3.phenylpropanoate.and.3..3.hydroxyphenyl.propanoate.degradation"
## [163] "PWY0.1297..superpathway.of.purine.deoxyribonucleosides.degradation"
## [164] "PWY0.1298..superpathway.of.pyrimidine.deoxyribonucleosides.degradation"
## [165] "PWY0.1338..polymyxin.resistance"
## [166] "PWY0.1415..superpathway.of.heme.biosynthesis.from.uroporphyrinogen.III"
## [167] "PWY0.1479..tRNA.processing"
## [168] "PWY0.1533..methylphosphonate.degradation.I"
## [169] "PWY0.41..allantoin.degradation.IV..anaerobic."
## [170] "PWY0.42..2.methylcitrate.cycle.I"
## [171] "PWY0.781..aspartate.superpathway"
## [172] "PWY0.862...5Z..dodec.5.enoate.biosynthesis"
## [173] "PWY0.881..superpathway.of.fatty.acid.biosynthesis.I..E..coli."
## [174] "PWY3O.355..stearate.biosynthesis.III..fungi."
## [175] "PWY4LZ.257..superpathway.of.fermentation..Chlamydomonas.reinhardtii."
## [176] "PWY66.389..phytol.degradation"
## [177] "PWY66.391..fatty.acid..beta..oxidation.VI..peroxisome."
## [178] "PWY66.398..TCA.cycle.III..animals."
## [179] "PWY66.409..superpathway.of.purine.nucleotide.salvage"
## [180] "PWYG.321..mycolate.biosynthesis"
## [181] "PYRIDNUCSAL.PWY..NAD.salvage.pathway.I"
## [182] "REDCITCYC..TCA.cycle.VIII..helicobacter."
## [183] "SALVADEHYPOX.PWY..adenosine.nucleotides.degradation.II"
## [184] "SO4ASSIM.PWY..sulfate.reduction.I..assimilatory."
## [185] "SULFATE.CYS.PWY..superpathway.of.sulfate.assimilation.and.cysteine.biosynthesis"
## [186] "TCA.GLYOX.BYPASS..superpathway.of.glyoxylate.bypass.and.TCA"
## [187] "THREOCAT.PWY..superpathway.of.L.threonine.metabolism"
## [188] "UBISYN.PWY..superpathway.of.ubiquinol.8.biosynthesis..prokaryotic."
## [189] "URDEGR.PWY..superpathway.of.allantoin.degradation.in.plants"
## [190] "X3.HYDROXYPHENYLACETATE.DEGRADATION.PWY..4.hydroxyphenylacetate.degradation"
############
# Run MSEA #
############
MSEA <- run_MSEA(microbeSet, results$feature)
MSEA <- MSEA[
, c('Set', 'Freq', 'ES', setdiff(names(MSEA), c('Set', 'Freq', 'ES')))]
colnames(MSEA) <- c('ID', 'Size', 'pval', 'qval')
MSEA$ID <- paste(MSEA$ID, ' (', MSEA$Size, ')', sep = '')
########
# Plot #
########
p <- MSEA |>
arrange(-pval) |>
mutate(ID = factor(ID, levels = ID)) |>
ggplot(aes(y = -log10(pval), x = ID)) +
geom_bar(stat = "identity", fill = 'cornflowerblue') + theme_bw() +
coord_flip() +
ggtitle('Statistically significant modules associated with disease') +
xlab('') +
ylab('MSEA enrichment score')
p
Based on the MSEA results, we obtain 4 enriched modules of microbial pathways. We can similarly examine the members of the top enriched modules.
A.5 Print the most significant modules for pathway abundance data
# Print the most significant modules
microbeSet[["MEpurple"]]
## NULL
microbeSet[["MEbrown"]]
## [1] "GLCMANNANAUT.PWY..superpathway.of.N.acetylglucosamine..N.acetylmannosamine.and.N.acetylneuraminate.degradation"
## [2] "GLYCOLYSIS.E.D..superpathway.of.glycolysis.and.Entner.Doudoroff"
## [3] "METH.ACETATE.PWY..methanogenesis.from.acetate"
## [4] "PWY.5100..pyruvate.fermentation.to.acetate.and.lactate.II"
## [5] "PWY.5104..L.isoleucine.biosynthesis.IV"
## [6] "PWY.5177..glutaryl.CoA.degradation"
## [7] "PWY.5690..TCA.cycle.II..plants.and.fungi."
## [8] "PWY.6470..peptidoglycan.biosynthesis.V...beta..lactam.resistance."
## [9] "PWY.6527..stachyose.degradation"
## [10] "PWY.6595..superpathway.of.guanosine.nucleotides.degradation..plants."
## [11] "PWY.6608..guanosine.nucleotides.degradation.III"
## [12] "PWY.7196..superpathway.of.pyrimidine.ribonucleosides.salvage"
## [13] "PWY.7198..pyrimidine.deoxyribonucleotides.de.novo.biosynthesis.IV"
## [14] "PWY0.1061..superpathway.of.L.alanine.biosynthesis"
## [15] "PWY0.1261..anhydromuropeptides.recycling"
## [16] "PWY66.400..glycolysis.VI..metazoan."
## [17] "TCA..TCA.cycle.I..prokaryotic."
## [18] "UDPNAGSYN.PWY..UDP.N.acetyl.D.glucosamine.biosynthesis.I"