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"
## 2025-04-09 20:45:50.424447 INFO::Writing function arguments to log file
## 2025-04-09 20:45:50.439708 INFO::Verifying options selected are valid
## 2025-04-09 20:45:50.467151 INFO::Determining format of input files
## 2025-04-09 20:45:50.46774 INFO::Input format is data samples as rows and metadata samples as rows
## 2025-04-09 20:45:50.47384 INFO::Formula for fixed effects: expr ~ disease + age + antibiotics_current_use
## 2025-04-09 20:45:50.474528 INFO::Factor detected for categorial metadata 'disease'. Provide a reference argument or manually set factor ordering to change reference level.
## 2025-04-09 20:45:50.475165 INFO::Filter data based on min abundance and min prevalence
## 2025-04-09 20:45:50.47562 INFO::Total samples in data: 136
## 2025-04-09 20:45:50.47606 INFO::Min samples required with min abundance for a feature not to be filtered: 13.600000
## 2025-04-09 20:45:50.481983 INFO::Total filtered features: 458
## 2025-04-09 20:45:50.482704 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
## 2025-04-09 20:45:50.485536 INFO::Total filtered features with variance filtering: 0
## 2025-04-09 20:45:50.486066 INFO::Filtered feature names from variance filtering:
## 2025-04-09 20:45:50.486507 INFO::Running selected normalization method: NONE
## 2025-04-09 20:45:50.48699 INFO::Applying z-score to standardize continuous metadata
## 2025-04-09 20:45:50.491154 INFO::Running selected transform method: LOG
## 2025-04-09 20:45:50.494049 INFO::Running selected analysis method: LM
## 2025-04-09 20:45:50.498256 INFO::Fitting model to feature number 1, species.Phocaeicola.vulgatus
## 2025-04-09 20:45:50.504241 INFO::Fitting model to feature number 2, species.Bacteroides.uniformis
## 2025-04-09 20:45:50.506711 INFO::Fitting model to feature number 3, species.Bacteroides.thetaiotaomicron
## 2025-04-09 20:45:50.50909 INFO::Fitting model to feature number 4, species.Faecalibacterium.prausnitzii
## 2025-04-09 20:45:50.511525 INFO::Fitting model to feature number 5, species.Roseburia.faecis
## 2025-04-09 20:45:50.513843 INFO::Fitting model to feature number 6, species.Bacteroides.caccae
## 2025-04-09 20:45:50.516134 INFO::Fitting model to feature number 7, species.Enterocloster.clostridioformis
## 2025-04-09 20:45:50.538138 INFO::Fitting model to feature number 8, species.Bacteroides.fragilis
## 2025-04-09 20:45:50.540677 INFO::Fitting model to feature number 9, species.Fusicatenibacter.saccharivorans
## 2025-04-09 20:45:50.543013 INFO::Fitting model to feature number 10, species.Flavonifractor.plautii
## 2025-04-09 20:45:50.545405 INFO::Fitting model to feature number 11, species.Dialister.invisus
## 2025-04-09 20:45:50.547677 INFO::Fitting model to feature number 12, species.Ruminococcus.bicirculans
## 2025-04-09 20:45:50.549942 INFO::Fitting model to feature number 13, species.Blautia.sp..CAG.257
## 2025-04-09 20:45:50.552221 INFO::Fitting model to feature number 14, species..Ruminococcus..gnavus
## 2025-04-09 20:45:50.554502 INFO::Fitting model to feature number 15, species.Dorea.longicatena
## 2025-04-09 20:45:50.556767 INFO::Fitting model to feature number 16, species.Anaerobutyricum.hallii
## 2025-04-09 20:45:50.559068 INFO::Fitting model to feature number 17, species.Enterocloster.bolteae
## 2025-04-09 20:45:50.561373 INFO::Fitting model to feature number 18, species.Eubacterium.sp..CAG.38
## 2025-04-09 20:45:50.563659 INFO::Fitting model to feature number 19, species.Lacrimispora.saccharolytica
## 2025-04-09 20:45:50.565946 INFO::Fitting model to feature number 20, species.Intestinimonas.butyriciproducens
## 2025-04-09 20:45:50.568256 INFO::Fitting model to feature number 21, species.Anaerostipes.hadrus
## 2025-04-09 20:45:50.570549 INFO::Fitting model to feature number 22, species.Anaerotignum.lactatifermentans
## 2025-04-09 20:45:50.572809 INFO::Fitting model to feature number 23, species.Ruthenibacterium.lactatiformans
## 2025-04-09 20:45:50.575116 INFO::Fitting model to feature number 24, species.Lawsonibacter.asaccharolyticus
## 2025-04-09 20:45:50.577427 INFO::Fitting model to feature number 25, species.Clostridium.bolteae.CAG.59
## 2025-04-09 20:45:50.579749 INFO::Fitting model to feature number 26, species..Clostridium..symbiosum
## 2025-04-09 20:45:50.582078 INFO::Fitting model to feature number 27, species.Anaerotruncus.colihominis
## 2025-04-09 20:45:50.584407 INFO::Fitting model to feature number 28, species.Agathobaculum.butyriciproducens
## 2025-04-09 20:45:50.586677 INFO::Fitting model to feature number 29, species.Escherichia.coli
## 2025-04-09 20:45:50.588955 INFO::Fitting model to feature number 30, species.Eisenbergiella.massiliensis
## 2025-04-09 20:45:50.591272 INFO::Fitting model to feature number 31, species.Enterocloster.citroniae
## 2025-04-09 20:45:50.593544 INFO::Fitting model to feature number 32, species.Bacteroides.stercoris
## 2025-04-09 20:45:50.595788 INFO::Fitting model to feature number 33, species.Monoglobus.pectinilyticus
## 2025-04-09 20:45:50.598068 INFO::Fitting model to feature number 34, species.Alistipes.putredinis
## 2025-04-09 20:45:50.600327 INFO::Fitting model to feature number 35, species.Parabacteroides.distasonis
## 2025-04-09 20:45:50.602579 INFO::Fitting model to feature number 36, species.Roseburia.hominis
## 2025-04-09 20:45:50.604832 INFO::Fitting model to feature number 37, species.Bifidobacterium.longum
## 2025-04-09 20:45:50.60713 INFO::Fitting model to feature number 38, species..Eubacterium..siraeum
## 2025-04-09 20:45:50.609408 INFO::Fitting model to feature number 39, species.Parabacteroides.merdae
## 2025-04-09 20:45:50.611652 INFO::Fitting model to feature number 40, species.Roseburia.inulinivorans
## 2025-04-09 20:45:50.613896 INFO::Fitting model to feature number 41, species.Bacteroides.cellulosilyticus
## 2025-04-09 20:45:50.61617 INFO::Fitting model to feature number 42, species.Bacteroides.ovatus
## 2025-04-09 20:45:50.618465 INFO::Fitting model to feature number 43, species.Blautia.wexlerae
## 2025-04-09 20:45:50.620729 INFO::Fitting model to feature number 44, species.Bifidobacterium.adolescentis
## 2025-04-09 20:45:50.623029 INFO::Fitting model to feature number 45, species.Lachnospira.eligens
## 2025-04-09 20:45:50.625279 INFO::Fitting model to feature number 46, species..Clostridium..leptum
## 2025-04-09 20:45:50.627538 INFO::Fitting model to feature number 47, species.Eggerthella.lenta
## 2025-04-09 20:45:50.629791 INFO::Fitting model to feature number 48, species.Bacteroides.xylanisolvens
## 2025-04-09 20:45:50.632063 INFO::Fitting model to feature number 49, species.Phocaeicola.dorei
## 2025-04-09 20:45:50.634321 INFO::Fitting model to feature number 50, species.Enterocloster.lavalensis
## 2025-04-09 20:45:50.636592 INFO::Fitting model to feature number 51, species..Eubacterium..rectale
## 2025-04-09 20:45:50.638869 INFO::Fitting model to feature number 52, species.Akkermansia.muciniphila
## 2025-04-09 20:45:50.64116 INFO::Fitting model to feature number 53, species.Acidaminococcus.intestini
## 2025-04-09 20:45:50.643412 INFO::Fitting model to feature number 54, species..Ruminococcus..torques
## 2025-04-09 20:45:50.645672 INFO::Fitting model to feature number 55, species.Bacteroides.salyersiae
## 2025-04-09 20:45:50.647992 INFO::Fitting model to feature number 56, species.Sellimonas.intestinalis
## 2025-04-09 20:45:50.650257 INFO::Fitting model to feature number 57, species.Bacteroides.faecis
## 2025-04-09 20:45:50.652545 INFO::Fitting model to feature number 58, species.Roseburia.intestinalis
## 2025-04-09 20:45:50.654834 INFO::Fitting model to feature number 59, species.Collinsella.aerofaciens
## 2025-04-09 20:45:50.657112 INFO::Fitting model to feature number 60, species.Bacteroides.intestinalis
## 2025-04-09 20:45:50.659388 INFO::Fitting model to feature number 61, species.Bacteroides.faecis.CAG.32
## 2025-04-09 20:45:50.661677 INFO::Fitting model to feature number 62, species..Ruminococcus..lactaris
## 2025-04-09 20:45:50.663971 INFO::Fitting model to feature number 63, species.Prevotella.copri
## 2025-04-09 20:45:50.666267 INFO::Fitting model to feature number 64, species.Eisenbergiella.tayi
## 2025-04-09 20:45:50.668559 INFO::Fitting model to feature number 65, species.Klebsiella.pneumoniae
## 2025-04-09 20:45:50.670844 INFO::Fitting model to feature number 66, species.Intestinibacter.bartlettii
## 2025-04-09 20:45:50.673171 INFO::Fitting model to feature number 67, species.Erysipelatoclostridium.ramosum
## 2025-04-09 20:45:50.675456 INFO::Fitting model to feature number 68, species.Barnesiella.intestinihominis
## 2025-04-09 20:45:50.677774 INFO::Fitting model to feature number 69, species.Blautia.obeum
## 2025-04-09 20:45:50.68008 INFO::Fitting model to feature number 70, species.Bacteroides.finegoldii
## 2025-04-09 20:45:50.68236 INFO::Fitting model to feature number 71, species.Parasutterella.excrementihominis
## 2025-04-09 20:45:50.684668 INFO::Fitting model to feature number 72, species.Phascolarctobacterium.faecium
## 2025-04-09 20:45:50.686945 INFO::Fitting model to feature number 73, species.Lachnospira.pectinoschiza
## 2025-04-09 20:45:50.689254 INFO::Fitting model to feature number 74, species.Clostridium.sp..CAG.58
## 2025-04-09 20:45:50.691532 INFO::Fitting model to feature number 75, species.Bilophila.wadsworthia
## 2025-04-09 20:45:50.693832 INFO::Fitting model to feature number 76, species.Turicimonas.muris
## 2025-04-09 20:45:50.696152 INFO::Fitting model to feature number 77, species.Proteobacteria.bacterium.CAG.139
## 2025-04-09 20:45:50.698446 INFO::Fitting model to feature number 78, species.Anaeromassilibacillus.sp..An250
## 2025-04-09 20:45:50.700732 INFO::Fitting model to feature number 79, species.Hungatella.hathewayi
## 2025-04-09 20:45:50.703084 INFO::Fitting model to feature number 80, species.Alistipes.finegoldii
## 2025-04-09 20:45:50.705395 INFO::Fitting model to feature number 81, species.Ruminococcus.bromii
## 2025-04-09 20:45:50.707676 INFO::Fitting model to feature number 82, species.Odoribacter.splanchnicus
## 2025-04-09 20:45:50.709971 INFO::Fitting model to feature number 83, species.Butyricimonas.virosa
## 2025-04-09 20:45:50.712242 INFO::Fitting model to feature number 84, species.Oscillibacter.sp..CAG.241
## 2025-04-09 20:45:50.714554 INFO::Fitting model to feature number 85, species.Alistipes.indistinctus
## 2025-04-09 20:45:50.716861 INFO::Fitting model to feature number 86, species.Coprococcus.comes
## 2025-04-09 20:45:50.719173 INFO::Fitting model to feature number 87, species.Gemmiger.formicilis
## 2025-04-09 20:45:50.721446 INFO::Fitting model to feature number 88, species.Holdemania.filiformis
## 2025-04-09 20:45:50.723748 INFO::Fitting model to feature number 89, species.Firmicutes.bacterium.CAG.83
## 2025-04-09 20:45:50.726043 INFO::Fitting model to feature number 90, species.Dorea.formicigenerans
## 2025-04-09 20:45:50.728334 INFO::Fitting model to feature number 91, species.Collinsella.intestinalis
## 2025-04-09 20:45:50.730631 INFO::Fitting model to feature number 92, species.Oscillibacter.sp..57_20
## 2025-04-09 20:45:50.733028 INFO::Fitting model to feature number 93, species.Firmicutes.bacterium.CAG.94
## 2025-04-09 20:45:50.735311 INFO::Fitting model to feature number 94, species.Dielma.fastidiosa
## 2025-04-09 20:45:50.737615 INFO::Fitting model to feature number 95, species.Roseburia.sp..CAG.471
## 2025-04-09 20:45:50.739912 INFO::Fitting model to feature number 96, species..Clostridium..innocuum
## 2025-04-09 20:45:50.742238 INFO::Fitting model to feature number 97, species.Haemophilus.parainfluenzae
## 2025-04-09 20:45:50.744551 INFO::Fitting model to feature number 98, species.Veillonella.dispar
## 2025-04-09 20:45:50.746855 INFO::Fitting model to feature number 99, species.Veillonella.parvula
## 2025-04-09 20:45:50.749149 INFO::Fitting model to feature number 100, species.Veillonella.infantium
## 2025-04-09 20:45:50.751468 INFO::Fitting model to feature number 101, species.Streptococcus.salivarius
## 2025-04-09 20:45:50.75376 INFO::Fitting model to feature number 102, species.Enterocloster.aldenensis
## 2025-04-09 20:45:50.756173 INFO::Fitting model to feature number 103, species.Veillonella.atypica
## 2025-04-09 20:45:50.758501 INFO::Fitting model to feature number 104, species.Phocaeicola.plebeius
## 2025-04-09 20:45:50.760805 INFO::Fitting model to feature number 105, species.Paraprevotella.xylaniphila
## 2025-04-09 20:45:50.763129 INFO::Fitting model to feature number 106, species.Bacteroides.eggerthii
## 2025-04-09 20:45:50.765412 INFO::Fitting model to feature number 107, species.Alistipes.shahii
## 2025-04-09 20:45:50.767715 INFO::Fitting model to feature number 108, species.Butyricimonas.synergistica
## 2025-04-09 20:45:50.770027 INFO::Fitting model to feature number 109, species.Haemophilus.sp..HMSC71H05
## 2025-04-09 20:45:50.772361 INFO::Fitting model to feature number 110, species.Eubacterium.ramulus
## 2025-04-09 20:45:50.77467 INFO::Fitting model to feature number 111, species.Coprobacter.fastidiosus
## 2025-04-09 20:45:50.776996 INFO::Fitting model to feature number 112, species.Lactobacillus.rogosae
## 2025-04-09 20:45:50.779443 INFO::Fitting model to feature number 113, species.Phocaeicola.massiliensis
## 2025-04-09 20:45:50.781739 INFO::Fitting model to feature number 114, species.Streptococcus.parasanguinis
## 2025-04-09 20:45:50.784078 INFO::Fitting model to feature number 115, species.Ruminococcaceae.bacterium.D16
## 2025-04-09 20:45:50.78638 INFO::Fitting model to feature number 116, species.Veillonella.sp..T11011.6
## 2025-04-09 20:45:50.788738 INFO::Fitting model to feature number 117, species.Klebsiella.variicola
## 2025-04-09 20:45:50.791126 INFO::Fitting model to feature number 118, species.Bacteroides.galacturonicus
## 2025-04-09 20:45:50.793442 INFO::Fitting model to feature number 119, species.Clostridium.sp..CAG.299
## 2025-04-09 20:45:50.795781 INFO::Fitting model to feature number 120, species.Eubacterium.ventriosum
## 2025-04-09 20:45:50.798175 INFO::Fitting model to feature number 121, species.Bifidobacterium.bifidum
## 2025-04-09 20:45:50.800602 INFO::Fitting model to feature number 122, species.Bifidobacterium.pseudocatenulatum
## 2025-04-09 20:45:50.8029 INFO::Fitting model to feature number 123, species.Coprococcus.eutactus
## 2025-04-09 20:45:50.805242 INFO::Fitting model to feature number 124, species.Eubacterium.sp..CAG.251
## 2025-04-09 20:45:50.807571 INFO::Fitting model to feature number 125, species.Phocaeicola.coprocola
## 2025-04-09 20:45:50.809942 INFO::Fitting model to feature number 126, species.Paraprevotella.clara
## 2025-04-09 20:45:50.812255 INFO::Fitting model to feature number 127, species.Coprococcus.catus
## 2025-04-09 20:45:50.832921 INFO::Counting total values for each feature
## 2025-04-09 20:45:50.844235 INFO::Writing filtered data to file output_species/features/filtered_data.tsv
## 2025-04-09 20:45:50.853205 INFO::Writing filtered, normalized data to file output_species/features/filtered_data_norm.tsv
## 2025-04-09 20:45:50.861754 INFO::Writing filtered, normalized, transformed data to file output_species/features/filtered_data_norm_transformed.tsv
## 2025-04-09 20:45:50.874564 INFO::Writing residuals to file output_species/fits/residuals.rds
## 2025-04-09 20:45:50.879971 INFO::Writing fitted values to file output_species/fits/fitted.rds
## 2025-04-09 20:45:50.88476 INFO::Writing all results to file (ordered by increasing q-values): output_species/all_results.tsv
## 2025-04-09 20:45:50.887107 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
## 2025-04-09 20:45:50.887921 INFO::Writing heatmap of significant results to file: output_species/heatmap.pdf
## 2025-04-09 20:45:51.005408 INFO::Writing association plots (one for each significant association) to output folder: output_species
## 2025-04-09 20:45:51.008067 INFO::Plotting associations from most to least significant, grouped by metadata
## 2025-04-09 20:45:51.008619 INFO::Plotting data for metadata number 1, age
## 2025-04-09 20:45:51.00953 INFO::Creating scatter plot for continuous data, age vs species.Alistipes.indistinctus
## 2025-04-09 20:45:51.155603 INFO::Creating scatter plot for continuous data, age vs species.Ruminococcus.bicirculans
## 2025-04-09 20:45:51.362712 INFO::Creating scatter plot for continuous data, age vs species.Lacrimispora.saccharolytica
## 2025-04-09 20:45:51.544746 INFO::Creating scatter plot for continuous data, age vs species.Ruminococcus.bromii
## 2025-04-09 20:45:51.672616 INFO::Creating scatter plot for continuous data, age vs species.Bifidobacterium.pseudocatenulatum
## 2025-04-09 20:45:51.807381 INFO::Creating scatter plot for continuous data, age vs species..Ruminococcus..gnavus
## 2025-04-09 20:45:51.936795 INFO::Creating scatter plot for continuous data, age vs species.Lachnospira.eligens
## 2025-04-09 20:45:52.090346 INFO::Creating scatter plot for continuous data, age vs species.Haemophilus.parainfluenzae
## 2025-04-09 20:45:52.226714 INFO::Creating scatter plot for continuous data, age vs species.Butyricimonas.virosa
## 2025-04-09 20:45:52.356314 INFO::Creating scatter plot for continuous data, age vs species.Lawsonibacter.asaccharolyticus
## 2025-04-09 20:45:52.48679 INFO::Creating scatter plot for continuous data, age vs species..Eubacterium..siraeum
## 2025-04-09 20:45:52.619277 INFO::Creating scatter plot for continuous data, age vs species.Butyricimonas.synergistica
## 2025-04-09 20:45:52.765693 INFO::Creating scatter plot for continuous data, age vs species.Monoglobus.pectinilyticus
## 2025-04-09 20:45:52.892475 INFO::Creating scatter plot for continuous data, age vs species.Veillonella.atypica
## 2025-04-09 20:45:54.51955 INFO::Plotting data for metadata number 2, disease
## 2025-04-09 20:45:54.520783 INFO::Creating boxplot for categorical data, disease vs species.Alistipes.putredinis
## 2025-04-09 20:45:54.676115 INFO::Creating boxplot for categorical data, disease vs species.Gemmiger.formicilis
## 2025-04-09 20:45:54.808434 INFO::Creating boxplot for categorical data, disease vs species..Ruminococcus..torques
## 2025-04-09 20:45:54.927171 INFO::Creating boxplot for categorical data, disease vs species.Ruminococcus.bicirculans
## 2025-04-09 20:45:55.062424 INFO::Creating boxplot for categorical data, disease vs species.Sellimonas.intestinalis
## 2025-04-09 20:45:55.17959 INFO::Creating boxplot for categorical data, disease vs species..Clostridium..leptum
## 2025-04-09 20:45:55.298591 INFO::Creating boxplot for categorical data, disease vs species.Alistipes.shahii
## 2025-04-09 20:45:56.421415 INFO::Plotting data for metadata number 3, antibiotics_current_use
## 2025-04-09 20:45:56.422906 INFO::Creating boxplot for categorical data, antibiotics_current_use vs species.Coprobacter.fastidiosus
## 2025-04-09 20:45:56.544976 INFO::Creating boxplot for categorical data, antibiotics_current_use vs species..Eubacterium..rectale
## 2025-04-09 20:45:56.677417 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"
## 2025-04-09 20:46:20.749122 INFO::Writing function arguments to log file
## 2025-04-09 20:46:20.752838 INFO::Verifying options selected are valid
## 2025-04-09 20:46:20.753339 INFO::Determining format of input files
## 2025-04-09 20:46:20.753826 INFO::Input format is data samples as rows and metadata samples as rows
## 2025-04-09 20:46:20.759381 INFO::Formula for fixed effects: expr ~ disease + age + antibiotics_current_use
## 2025-04-09 20:46:20.760095 INFO::Factor detected for categorial metadata 'disease'. Provide a reference argument or manually set factor ordering to change reference level.
## 2025-04-09 20:46:20.760739 INFO::Filter data based on min abundance and min prevalence
## 2025-04-09 20:46:20.761228 INFO::Total samples in data: 136
## 2025-04-09 20:46:20.76165 INFO::Min samples required with min abundance for a feature not to be filtered: 13.600000
## 2025-04-09 20:46:20.766843 INFO::Total filtered features: 113
## 2025-04-09 20:46:20.767463 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
## 2025-04-09 20:46:20.773412 INFO::Total filtered features with variance filtering: 0
## 2025-04-09 20:46:20.773956 INFO::Filtered feature names from variance filtering:
## 2025-04-09 20:46:20.774419 INFO::Running selected normalization method: NONE
## 2025-04-09 20:46:20.774834 INFO::Applying z-score to standardize continuous metadata
## 2025-04-09 20:46:20.778363 INFO::Running selected transform method: LOG
## 2025-04-09 20:46:20.785336 INFO::Running selected analysis method: LM
## 2025-04-09 20:46:20.785901 INFO::Fitting model to feature number 1, PWY.1042..glycolysis.IV..plant.cytosol.
## 2025-04-09 20:46:20.788623 INFO::Fitting model to feature number 2, DTDPRHAMSYN.PWY..dTDP.L.rhamnose.biosynthesis.I
## 2025-04-09 20:46:20.791064 INFO::Fitting model to feature number 3, PWY.5695..urate.biosynthesis.inosine.5..phosphate.degradation
## 2025-04-09 20:46:20.793438 INFO::Fitting model to feature number 4, PWY.6936..seleno.amino.acid.biosynthesis
## 2025-04-09 20:46:20.79578 INFO::Fitting model to feature number 5, ILEUSYN.PWY..L.isoleucine.biosynthesis.I..from.threonine.
## 2025-04-09 20:46:20.798204 INFO::Fitting model to feature number 6, PWY.7111..pyruvate.fermentation.to.isobutanol..engineered.
## 2025-04-09 20:46:20.800585 INFO::Fitting model to feature number 7, VALSYN.PWY..L.valine.biosynthesis
## 2025-04-09 20:46:20.802932 INFO::Fitting model to feature number 8, PWY.6609..adenine.and.adenosine.salvage.III
## 2025-04-09 20:46:20.805307 INFO::Fitting model to feature number 9, PWY.6737..starch.degradation.V
## 2025-04-09 20:46:20.80766 INFO::Fitting model to feature number 10, PWY.7219..adenosine.ribonucleotides.de.novo.biosynthesis
## 2025-04-09 20:46:20.810012 INFO::Fitting model to feature number 11, PWY0.1586..peptidoglycan.maturation..meso.diaminopimelate.containing.
## 2025-04-09 20:46:20.812356 INFO::Fitting model to feature number 12, ASPASN.PWY..superpathway.of.L.aspartate.and.L.asparagine.biosynthesis
## 2025-04-09 20:46:20.814684 INFO::Fitting model to feature number 13, PWY.5973..cis.vaccenate.biosynthesis
## 2025-04-09 20:46:20.81704 INFO::Fitting model to feature number 14, PWY.7221..guanosine.ribonucleotides.de.novo.biosynthesis
## 2025-04-09 20:46:20.819373 INFO::Fitting model to feature number 15, PWY.5686..UMP.biosynthesis
## 2025-04-09 20:46:20.821703 INFO::Fitting model to feature number 16, X1CMET2.PWY..N10.formyl.tetrahydrofolate.biosynthesis
## 2025-04-09 20:46:20.824075 INFO::Fitting model to feature number 17, PWY.6122..5.aminoimidazole.ribonucleotide.biosynthesis.II
## 2025-04-09 20:46:20.826388 INFO::Fitting model to feature number 18, PWY.6277..superpathway.of.5.aminoimidazole.ribonucleotide.biosynthesis
## 2025-04-09 20:46:20.828705 INFO::Fitting model to feature number 19, PWY.6385..peptidoglycan.biosynthesis.III..mycobacteria.
## 2025-04-09 20:46:20.831037 INFO::Fitting model to feature number 20, PWY.3841..folate.transformations.II
## 2025-04-09 20:46:20.833358 INFO::Fitting model to feature number 21, RIBOSYN2.PWY..flavin.biosynthesis.I..bacteria.and.plants.
## 2025-04-09 20:46:20.835701 INFO::Fitting model to feature number 22, PWY.6387..UDP.N.acetylmuramoyl.pentapeptide.biosynthesis.I..meso.diaminopimelate.containing.
## 2025-04-09 20:46:20.838057 INFO::Fitting model to feature number 23, THISYNARA.PWY..superpathway.of.thiamin.diphosphate.biosynthesis.III..eukaryotes.
## 2025-04-09 20:46:20.840403 INFO::Fitting model to feature number 24, PWY.7663..gondoate.biosynthesis..anaerobic.
## 2025-04-09 20:46:20.842827 INFO::Fitting model to feature number 25, PWY.6386..UDP.N.acetylmuramoyl.pentapeptide.biosynthesis.II..lysine.containing.
## 2025-04-09 20:46:20.845197 INFO::Fitting model to feature number 26, PWY.6700..queuosine.biosynthesis
## 2025-04-09 20:46:20.847521 INFO::Fitting model to feature number 27, PEPTIDOGLYCANSYN.PWY..peptidoglycan.biosynthesis.I..meso.diaminopimelate.containing.
## 2025-04-09 20:46:20.849843 INFO::Fitting model to feature number 28, TRNA.CHARGING.PWY..tRNA.charging
## 2025-04-09 20:46:20.852172 INFO::Fitting model to feature number 29, PWY.6121..5.aminoimidazole.ribonucleotide.biosynthesis.I
## 2025-04-09 20:46:20.854509 INFO::Fitting model to feature number 30, HISTSYN.PWY..L.histidine.biosynthesis
## 2025-04-09 20:46:20.856818 INFO::Fitting model to feature number 31, PWY.7229..superpathway.of.adenosine.nucleotides.de.novo.biosynthesis.I
## 2025-04-09 20:46:20.859155 INFO::Fitting model to feature number 32, PWY.7199..pyrimidine.deoxyribonucleosides.salvage
## 2025-04-09 20:46:20.861491 INFO::Fitting model to feature number 33, PANTO.PWY..phosphopantothenate.biosynthesis.I
## 2025-04-09 20:46:20.863818 INFO::Fitting model to feature number 34, PWY.2942..L.lysine.biosynthesis.III
## 2025-04-09 20:46:20.866191 INFO::Fitting model to feature number 35, PWY.7237..myo...chiro..and.scillo.inositol.degradation
## 2025-04-09 20:46:20.868519 INFO::Fitting model to feature number 36, PWY.6168..flavin.biosynthesis.III..fungi.
## 2025-04-09 20:46:20.870856 INFO::Fitting model to feature number 37, COA.PWY.1..coenzyme.A.biosynthesis.II..mammalian.
## 2025-04-09 20:46:20.873202 INFO::Fitting model to feature number 38, PWY.5667..CDP.diacylglycerol.biosynthesis.I
## 2025-04-09 20:46:20.875569 INFO::Fitting model to feature number 39, PWY0.1319..CDP.diacylglycerol.biosynthesis.II
## 2025-04-09 20:46:20.877909 INFO::Fitting model to feature number 40, PWY.5097..L.lysine.biosynthesis.VI
## 2025-04-09 20:46:20.880244 INFO::Fitting model to feature number 41, ANAGLYCOLYSIS.PWY..glycolysis.III..from.glucose.
## 2025-04-09 20:46:20.882624 INFO::Fitting model to feature number 42, PWY.6123..inosine.5..phosphate.biosynthesis.I
## 2025-04-09 20:46:20.884935 INFO::Fitting model to feature number 43, ARGININE.SYN4.PWY..L.ornithine.de.novo..biosynthesis
## 2025-04-09 20:46:20.887281 INFO::Fitting model to feature number 44, PWY.6163..chorismate.biosynthesis.from.3.dehydroquinate
## 2025-04-09 20:46:20.889595 INFO::Fitting model to feature number 45, THRESYN.PWY..superpathway.of.L.threonine.biosynthesis
## 2025-04-09 20:46:20.891908 INFO::Fitting model to feature number 46, PYRIDNUCSYN.PWY..NAD.biosynthesis.I..from.aspartate.
## 2025-04-09 20:46:20.894242 INFO::Fitting model to feature number 47, PWY.6124..inosine.5..phosphate.biosynthesis.II
## 2025-04-09 20:46:20.896558 INFO::Fitting model to feature number 48, PWY.6147..6.hydroxymethyl.dihydropterin.diphosphate.biosynthesis.I
## 2025-04-09 20:46:20.898881 INFO::Fitting model to feature number 49, PWY.7539..6.hydroxymethyl.dihydropterin.diphosphate.biosynthesis.III..Chlamydia.
## 2025-04-09 20:46:20.901212 INFO::Fitting model to feature number 50, PWY.6151..S.adenosyl.L.methionine.cycle.I
## 2025-04-09 20:46:20.903544 INFO::Fitting model to feature number 51, SER.GLYSYN.PWY..superpathway.of.L.serine.and.glycine.biosynthesis.I
## 2025-04-09 20:46:20.90587 INFO::Fitting model to feature number 52, PWY.6126..superpathway.of.adenosine.nucleotides.de.novo.biosynthesis.II
## 2025-04-09 20:46:20.908219 INFO::Fitting model to feature number 53, PANTOSYN.PWY..pantothenate.and.coenzyme.A.biosynthesis.I
## 2025-04-09 20:46:20.910546 INFO::Fitting model to feature number 54, PWY.7228..superpathway.of.guanosine.nucleotides.de.novo.biosynthesis.I
## 2025-04-09 20:46:20.912874 INFO::Fitting model to feature number 55, COA.PWY..coenzyme.A.biosynthesis.I
## 2025-04-09 20:46:20.91523 INFO::Fitting model to feature number 56, PWY.4242..pantothenate.and.coenzyme.A.biosynthesis.III
## 2025-04-09 20:46:20.917557 INFO::Fitting model to feature number 57, PWY.6703..preQ0.biosynthesis
## 2025-04-09 20:46:20.919878 INFO::Fitting model to feature number 58, THISYN.PWY..superpathway.of.thiamin.diphosphate.biosynthesis.I
## 2025-04-09 20:46:20.922264 INFO::Fitting model to feature number 59, HISDEG.PWY..L.histidine.degradation.I
## 2025-04-09 20:46:20.924623 INFO::Fitting model to feature number 60, PWY.5659..GDP.mannose.biosynthesis
## 2025-04-09 20:46:20.926923 INFO::Fitting model to feature number 61, PWY.5030..L.histidine.degradation.III
## 2025-04-09 20:46:20.929288 INFO::Fitting model to feature number 62, PWY.5484..glycolysis.II..from.fructose.6.phosphate.
## 2025-04-09 20:46:20.931613 INFO::Fitting model to feature number 63, PWY.3001..superpathway.of.L.isoleucine.biosynthesis.I
## 2025-04-09 20:46:20.933981 INFO::Fitting model to feature number 64, PWY.6125..superpathway.of.guanosine.nucleotides.de.novo.biosynthesis.II
## 2025-04-09 20:46:20.936307 INFO::Fitting model to feature number 65, TRPSYN.PWY..L.tryptophan.biosynthesis
## 2025-04-09 20:46:20.938619 INFO::Fitting model to feature number 66, GLYCOLYSIS..glycolysis.I..from.glucose.6.phosphate.
## 2025-04-09 20:46:20.940938 INFO::Fitting model to feature number 67, PWY.724..superpathway.of.L.lysine..L.threonine.and.L.methionine.biosynthesis.II
## 2025-04-09 20:46:20.943301 INFO::Fitting model to feature number 68, PWY.6897..thiamin.salvage.II
## 2025-04-09 20:46:20.945661 INFO::Fitting model to feature number 69, BRANCHED.CHAIN.AA.SYN.PWY..superpathway.of.branched.amino.acid.biosynthesis
## 2025-04-09 20:46:20.948014 INFO::Fitting model to feature number 70, CALVIN.PWY..Calvin.Benson.Bassham.cycle
## 2025-04-09 20:46:20.950324 INFO::Fitting model to feature number 71, PWY.841..superpathway.of.purine.nucleotides.de.novo.biosynthesis.I
## 2025-04-09 20:46:20.952633 INFO::Fitting model to feature number 72, COMPLETE.ARO.PWY..superpathway.of.aromatic.amino.acid.biosynthesis
## 2025-04-09 20:46:20.954951 INFO::Fitting model to feature number 73, PWY.7220..adenosine.deoxyribonucleotides.de.novo.biosynthesis.II
## 2025-04-09 20:46:20.957274 INFO::Fitting model to feature number 74, PWY.7222..guanosine.deoxyribonucleotides.de.novo.biosynthesis.II
## 2025-04-09 20:46:20.959608 INFO::Fitting model to feature number 75, DENOVOPURINE2.PWY..superpathway.of.purine.nucleotides.de.novo.biosynthesis.II
## 2025-04-09 20:46:20.961913 INFO::Fitting model to feature number 76, PWY.7357..thiamin.formation.from.pyrithiamine.and.oxythiamine..yeast.
## 2025-04-09 20:46:20.964305 INFO::Fitting model to feature number 77, PWY.5103..L.isoleucine.biosynthesis.III
## 2025-04-09 20:46:20.966624 INFO::Fitting model to feature number 78, ARO.PWY..chorismate.biosynthesis.I
## 2025-04-09 20:46:20.968935 INFO::Fitting model to feature number 79, PWY.7282..4.amino.2.methyl.5.phosphomethylpyrimidine.biosynthesis..yeast.
## 2025-04-09 20:46:20.971267 INFO::Fitting model to feature number 80, PWY0.845..superpathway.of.pyridoxal.5..phosphate.biosynthesis.and.salvage
## 2025-04-09 20:46:20.973679 INFO::Fitting model to feature number 81, ANAEROFRUCAT.PWY..homolactic.fermentation
## 2025-04-09 20:46:20.976012 INFO::Fitting model to feature number 82, PWY.6892..thiazole.biosynthesis.I..E..coli.
## 2025-04-09 20:46:20.978327 INFO::Fitting model to feature number 83, RHAMCAT.PWY..L.rhamnose.degradation.I
## 2025-04-09 20:46:20.980651 INFO::Fitting model to feature number 84, PYRIDOXSYN.PWY..pyridoxal.5..phosphate.biosynthesis.I
## 2025-04-09 20:46:20.982993 INFO::Fitting model to feature number 85, PWY.1269..CMP.3.deoxy.D.manno.octulosonate.biosynthesis.I
## 2025-04-09 20:46:20.985314 INFO::Fitting model to feature number 86, PHOSLIPSYN.PWY..superpathway.of.phospholipid.biosynthesis.I..bacteria.
## 2025-04-09 20:46:20.987635 INFO::Fitting model to feature number 87, CITRULBIO.PWY..L.citrulline.biosynthesis
## 2025-04-09 20:46:20.989947 INFO::Fitting model to feature number 88, NAGLIPASYN.PWY..lipid.IVA.biosynthesis
## 2025-04-09 20:46:20.992276 INFO::Fitting model to feature number 89, BIOTIN.BIOSYNTHESIS.PWY..biotin.biosynthesis.I
## 2025-04-09 20:46:20.994585 INFO::Fitting model to feature number 90, PWY.5154..L.arginine.biosynthesis.III..via.N.acetyl.L.citrulline.
## 2025-04-09 20:46:20.996898 INFO::Fitting model to feature number 91, FASYN.ELONG.PWY..fatty.acid.elongation....saturated
## 2025-04-09 20:46:20.999239 INFO::Fitting model to feature number 92, PENTOSE.P.PWY..pentose.phosphate.pathway
## 2025-04-09 20:46:21.001549 INFO::Fitting model to feature number 93, PWYG.321..mycolate.biosynthesis
## 2025-04-09 20:46:21.003857 INFO::Fitting model to feature number 94, PWY.6519..8.amino.7.oxononanoate.biosynthesis.I
## 2025-04-09 20:46:21.006203 INFO::Fitting model to feature number 95, PWY.7664..oleate.biosynthesis.IV..anaerobic.
## 2025-04-09 20:46:21.008521 INFO::Fitting model to feature number 96, PWY.4981..L.proline.biosynthesis.II..from.arginine.
## 2025-04-09 20:46:21.010834 INFO::Fitting model to feature number 97, GLYCOGENSYNTH.PWY..glycogen.biosynthesis.I..from.ADP.D.Glucose.
## 2025-04-09 20:46:21.013179 INFO::Fitting model to feature number 98, PWY.7388..octanoyl..acyl.carrier.protein..biosynthesis..mitochondria..yeast.
## 2025-04-09 20:46:21.015507 INFO::Fitting model to feature number 99, NONOXIPENT.PWY..pentose.phosphate.pathway..non.oxidative.branch.
## 2025-04-09 20:46:21.017819 INFO::Fitting model to feature number 100, COBALSYN.PWY..adenosylcobalamin.salvage.from.cobinamide.I
## 2025-04-09 20:46:21.020154 INFO::Fitting model to feature number 101, PWY.5989..stearate.biosynthesis.II..bacteria.and.plants.
## 2025-04-09 20:46:21.022489 INFO::Fitting model to feature number 102, PWY.6282..palmitoleate.biosynthesis.I..from..5Z..dodec.5.enoate.
## 2025-04-09 20:46:21.024803 INFO::Fitting model to feature number 103, PWY0.862...5Z..dodec.5.enoate.biosynthesis
## 2025-04-09 20:46:21.027144 INFO::Fitting model to feature number 104, PWY.7400..L.arginine.biosynthesis.IV..archaebacteria.
## 2025-04-09 20:46:21.029464 INFO::Fitting model to feature number 105, ARGSYN.PWY..L.arginine.biosynthesis.I..via.L.ornithine.
## 2025-04-09 20:46:21.031791 INFO::Fitting model to feature number 106, PWY.4984..urea.cycle
## 2025-04-09 20:46:21.034181 INFO::Fitting model to feature number 107, FASYN.INITIAL.PWY..superpathway.of.fatty.acid.biosynthesis.initiation..E..coli.
## 2025-04-09 20:46:21.03651 INFO::Fitting model to feature number 108, PWY4FS.7..phosphatidylglycerol.biosynthesis.I..plastidic.
## 2025-04-09 20:46:21.038835 INFO::Fitting model to feature number 109, PWY4FS.8..phosphatidylglycerol.biosynthesis.II..non.plastidic.
## 2025-04-09 20:46:21.041232 INFO::Fitting model to feature number 110, ARGSYNBSUB.PWY..L.arginine.biosynthesis.II..acetyl.cycle.
## 2025-04-09 20:46:21.043683 INFO::Fitting model to feature number 111, PWY.6317..galactose.degradation.I..Leloir.pathway.
## 2025-04-09 20:46:21.046025 INFO::Fitting model to feature number 112, PWY66.422..D.galactose.degradation.V..Leloir.pathway.
## 2025-04-09 20:46:21.04834 INFO::Fitting model to feature number 113, GLUTORN.PWY..L.ornithine.biosynthesis
## 2025-04-09 20:46:21.050675 INFO::Fitting model to feature number 114, PWY.2941..L.lysine.biosynthesis.II
## 2025-04-09 20:46:21.053024 INFO::Fitting model to feature number 115, PWY0.1296..purine.ribonucleosides.degradation
## 2025-04-09 20:46:21.055344 INFO::Fitting model to feature number 116, NAD.BIOSYNTHESIS.II..NAD.salvage.pathway.II
## 2025-04-09 20:46:21.057744 INFO::Fitting model to feature number 117, HSERMETANA.PWY..L.methionine.biosynthesis.III
## 2025-04-09 20:46:21.060109 INFO::Fitting model to feature number 118, PWY0.162..superpathway.of.pyrimidine.ribonucleotides.de.novo.biosynthesis
## 2025-04-09 20:46:21.062446 INFO::Fitting model to feature number 119, PWY.7208..superpathway.of.pyrimidine.nucleobases.salvage
## 2025-04-09 20:46:21.064775 INFO::Fitting model to feature number 120, TEICHOICACID.PWY..teichoic.acid..poly.glycerol..biosynthesis
## 2025-04-09 20:46:21.067131 INFO::Fitting model to feature number 121, PWY.6305..putrescine.biosynthesis.IV
## 2025-04-09 20:46:21.069448 INFO::Fitting model to feature number 122, GLUCONEO.PWY..gluconeogenesis.I
## 2025-04-09 20:46:21.071768 INFO::Fitting model to feature number 123, PWY.621..sucrose.degradation.III..sucrose.invertase.
## 2025-04-09 20:46:21.074123 INFO::Fitting model to feature number 124, PWY.6901..superpathway.of.glucose.and.xylose.degradation
## 2025-04-09 20:46:21.076462 INFO::Fitting model to feature number 125, POLYISOPRENSYN.PWY..polyisoprenoid.biosynthesis..E..coli.
## 2025-04-09 20:46:21.078821 INFO::Fitting model to feature number 126, PWY.7323..superpathway.of.GDP.mannose.derived.O.antigen.building.blocks.biosynthesis
## 2025-04-09 20:46:21.081162 INFO::Fitting model to feature number 127, PWY.5941..glycogen.degradation.II..eukaryotic.
## 2025-04-09 20:46:21.083495 INFO::Fitting model to feature number 128, PWY.6527..stachyose.degradation
## 2025-04-09 20:46:21.085806 INFO::Fitting model to feature number 129, PWY0.1261..anhydromuropeptides.recycling
## 2025-04-09 20:46:21.088165 INFO::Fitting model to feature number 130, PWY66.400..glycolysis.VI..metazoan.
## 2025-04-09 20:46:21.090504 INFO::Fitting model to feature number 131, PWY0.166..superpathway.of.pyrimidine.deoxyribonucleotides.de.novo.biosynthesis..E..coli.
## 2025-04-09 20:46:21.09284 INFO::Fitting model to feature number 132, GLYCOLYSIS.E.D..superpathway.of.glycolysis.and.Entner.Doudoroff
## 2025-04-09 20:46:21.095184 INFO::Fitting model to feature number 133, PWY.7187..pyrimidine.deoxyribonucleotides.de.novo.biosynthesis.II
## 2025-04-09 20:46:21.097492 INFO::Fitting model to feature number 134, PWY.7456..mannan.degradation
## 2025-04-09 20:46:21.099819 INFO::Fitting model to feature number 135, PWY.7184..pyrimidine.deoxyribonucleotides.de.novo.biosynthesis.I
## 2025-04-09 20:46:21.102158 INFO::Fitting model to feature number 136, OANTIGEN.PWY..O.antigen.building.blocks.biosynthesis..E..coli.
## 2025-04-09 20:46:21.104486 INFO::Fitting model to feature number 137, COLANSYN.PWY..colanic.acid.building.blocks.biosynthesis
## 2025-04-09 20:46:21.106866 INFO::Fitting model to feature number 138, PWY.6545..pyrimidine.deoxyribonucleotides.de.novo.biosynthesis.III
## 2025-04-09 20:46:21.109215 INFO::Fitting model to feature number 139, PWY.6895..superpathway.of.thiamin.diphosphate.biosynthesis.II
## 2025-04-09 20:46:21.111537 INFO::Fitting model to feature number 140, PWY.6608..guanosine.nucleotides.degradation.III
## 2025-04-09 20:46:21.113875 INFO::Fitting model to feature number 141, TCA..TCA.cycle.I..prokaryotic.
## 2025-04-09 20:46:21.116244 INFO::Fitting model to feature number 142, PWY.6859..all.trans.farnesol.biosynthesis
## 2025-04-09 20:46:21.118551 INFO::Fitting model to feature number 143, PWY.5100..pyruvate.fermentation.to.acetate.and.lactate.II
## 2025-04-09 20:46:21.12087 INFO::Fitting model to feature number 144, PWY.6572..chondroitin.sulfate.degradation.I..bacterial.
## 2025-04-09 20:46:21.123253 INFO::Fitting model to feature number 145, PWY.6471..peptidoglycan.biosynthesis.IV..Enterococcus.faecium.
## 2025-04-09 20:46:21.125578 INFO::Fitting model to feature number 146, PWY.6470..peptidoglycan.biosynthesis.V...beta..lactam.resistance.
## 2025-04-09 20:46:21.127905 INFO::Fitting model to feature number 147, PWY.5188..tetrapyrrole.biosynthesis.I..from.glutamate.
## 2025-04-09 20:46:21.130248 INFO::Fitting model to feature number 148, GLUCUROCAT.PWY..superpathway.of..beta..D.glucuronide.and.D.glucuronate.degradation
## 2025-04-09 20:46:21.132647 INFO::Fitting model to feature number 149, PWY.6749..CMP.legionaminate.biosynthesis.I
## 2025-04-09 20:46:21.134999 INFO::Fitting model to feature number 150, P164.PWY..purine.nucleobases.degradation.I..anaerobic.
## 2025-04-09 20:46:21.137319 INFO::Fitting model to feature number 151, PWY.7198..pyrimidine.deoxyribonucleotides.de.novo.biosynthesis.IV
## 2025-04-09 20:46:21.139644 INFO::Fitting model to feature number 152, PWY.7211..superpathway.of.pyrimidine.deoxyribonucleotides.de.novo.biosynthesis
## 2025-04-09 20:46:21.141988 INFO::Fitting model to feature number 153, PWY66.409..superpathway.of.purine.nucleotide.salvage
## 2025-04-09 20:46:21.144319 INFO::Fitting model to feature number 154, GALACT.GLUCUROCAT.PWY..superpathway.of.hexuronide.and.hexuronate.degradation
## 2025-04-09 20:46:21.146638 INFO::Fitting model to feature number 155, UDPNAGSYN.PWY..UDP.N.acetyl.D.glucosamine.biosynthesis.I
## 2025-04-09 20:46:21.148948 INFO::Fitting model to feature number 156, PWY.6353..purine.nucleotides.degradation.II..aerobic.
## 2025-04-09 20:46:21.151289 INFO::Fitting model to feature number 157, PWY.7197..pyrimidine.deoxyribonucleotide.phosphorylation
## 2025-04-09 20:46:21.153625 INFO::Fitting model to feature number 158, PWY.7242..D.fructuronate.degradation
## 2025-04-09 20:46:21.155985 INFO::Fitting model to feature number 159, PWY.7196..superpathway.of.pyrimidine.ribonucleosides.salvage
## 2025-04-09 20:46:21.158326 INFO::Fitting model to feature number 160, PWY.5690..TCA.cycle.II..plants.and.fungi.
## 2025-04-09 20:46:21.160655 INFO::Fitting model to feature number 161, PWY.5177..glutaryl.CoA.degradation
## 2025-04-09 20:46:21.163006 INFO::Fitting model to feature number 162, PWY.6478..GDP.D.glycero..alpha..D.manno.heptose.biosynthesis
## 2025-04-09 20:46:21.165355 INFO::Fitting model to feature number 163, HEXITOLDEGSUPER.PWY..superpathway.of.hexitol.degradation..bacteria.
## 2025-04-09 20:46:21.168052 INFO::Fitting model to feature number 164, GALACTUROCAT.PWY..D.galacturonate.degradation.I
## 2025-04-09 20:46:21.170827 INFO::Fitting model to feature number 165, PWY.5104..L.isoleucine.biosynthesis.IV
## 2025-04-09 20:46:21.174584 INFO::Fitting model to feature number 166, PWY.5505..L.glutamate.and.L.glutamine.biosynthesis
## 2025-04-09 20:46:21.1779 INFO::Fitting model to feature number 167, P441.PWY..superpathway.of.N.acetylneuraminate.degradation
## 2025-04-09 20:46:21.181365 INFO::Fitting model to feature number 168, PWY.6606..guanosine.nucleotides.degradation.II
## 2025-04-09 20:46:21.183924 INFO::Fitting model to feature number 169, SALVADEHYPOX.PWY..adenosine.nucleotides.degradation.II
## 2025-04-09 20:46:21.186384 INFO::Fitting model to feature number 170, PWY.5005..biotin.biosynthesis.II
## 2025-04-09 20:46:21.188797 INFO::Fitting model to feature number 171, PWY.6549..L.glutamine.biosynthesis.III
## 2025-04-09 20:46:21.191219 INFO::Fitting model to feature number 172, GLCMANNANAUT.PWY..superpathway.of.N.acetylglucosamine..N.acetylmannosamine.and.N.acetylneuraminate.degradation
## 2025-04-09 20:46:21.193605 INFO::Fitting model to feature number 173, PWY0.1241..ADP.L.glycero..beta..D.manno.heptose.biosynthesis
## 2025-04-09 20:46:21.19602 INFO::Fitting model to feature number 174, PWY.6507..4.deoxy.L.threo.hex.4.enopyranuronate.degradation
## 2025-04-09 20:46:21.198375 INFO::Fitting model to feature number 175, GALACTARDEG.PWY..D.galactarate.degradation.I
## 2025-04-09 20:46:21.200741 INFO::Fitting model to feature number 176, GLUCARGALACTSUPER.PWY..superpathway.of.D.glucarate.and.D.galactarate.degradation
## 2025-04-09 20:46:21.203107 INFO::Fitting model to feature number 177, PWY.5676..acetyl.CoA.fermentation.to.butanoate.II
## 2025-04-09 20:46:21.205499 INFO::Fitting model to feature number 178, PWY.5347..superpathway.of.L.methionine.biosynthesis..transsulfuration.
## 2025-04-09 20:46:21.207845 INFO::Fitting model to feature number 179, PWY.5138..unsaturated..even.numbered.fatty.acid..beta..oxidation
## 2025-04-09 20:46:21.210207 INFO::Fitting model to feature number 180, MET.SAM.PWY..superpathway.of.S.adenosyl.L.methionine.biosynthesis
## 2025-04-09 20:46:21.212553 INFO::Fitting model to feature number 181, PWY66.399..gluconeogenesis.III
## 2025-04-09 20:46:21.214902 INFO::Fitting model to feature number 182, PWY0.1297..superpathway.of.purine.deoxyribonucleosides.degradation
## 2025-04-09 20:46:21.217294 INFO::Fitting model to feature number 183, METSYN.PWY..L.homoserine.and.L.methionine.biosynthesis
## 2025-04-09 20:46:21.219749 INFO::Fitting model to feature number 184, PWY.7332..superpathway.of.UDP.N.acetylglucosamine.derived.O.antigen.building.blocks.biosynthesis
## 2025-04-09 20:46:21.222125 INFO::Fitting model to feature number 185, PWY.6588..pyruvate.fermentation.to.acetone
## 2025-04-09 20:46:21.224481 INFO::Fitting model to feature number 186, PWY.6891..thiazole.biosynthesis.II..Bacillus.
## 2025-04-09 20:46:21.226871 INFO::Fitting model to feature number 187, GLUCARDEG.PWY..D.glucarate.degradation.I
## 2025-04-09 20:46:21.229232 INFO::Fitting model to feature number 188, METH.ACETATE.PWY..methanogenesis.from.acetate
## 2025-04-09 20:46:21.231564 INFO::Fitting model to feature number 189, PWY.7013..L.1.2.propanediol.degradation
## 2025-04-09 20:46:21.233903 INFO::Fitting model to feature number 190, PWY.6590..superpathway.of.Clostridium.acetobutylicum.acidogenic.fermentation
## 2025-04-09 20:46:21.236243 INFO::Fitting model to feature number 191, FAO.PWY..fatty.acid..beta..oxidation.I
## 2025-04-09 20:46:21.238626 INFO::Fitting model to feature number 192, PWY.6318..L.phenylalanine.degradation.IV..mammalian..via.side.chain.
## 2025-04-09 20:46:21.240983 INFO::Fitting model to feature number 193, CENTFERM.PWY..pyruvate.fermentation.to.butanoate
## 2025-04-09 20:46:21.243458 INFO::Fitting model to feature number 194, GOLPDLCAT.PWY..superpathway.of.glycerol.degradation.to.1.3.propanediol
## 2025-04-09 20:46:21.245815 INFO::Fitting model to feature number 195, PWY.5136..fatty.acid..beta..oxidation.II..peroxisome.
## 2025-04-09 20:46:21.248195 INFO::Fitting model to feature number 196, PWY66.391..fatty.acid..beta..oxidation.VI..peroxisome.
## 2025-04-09 20:46:21.250567 INFO::Fitting model to feature number 197, HOMOSER.METSYN.PWY..L.methionine.biosynthesis.I
## 2025-04-09 20:46:21.252907 INFO::Fitting model to feature number 198, METHGLYUT.PWY..superpathway.of.methylglyoxal.degradation
## 2025-04-09 20:46:21.255275 INFO::Fitting model to feature number 199, PWY.7288..fatty.acid..beta..oxidation..peroxisome..yeast.
## 2025-04-09 20:46:21.257644 INFO::Fitting model to feature number 200, PWY.7383..anaerobic.energy.metabolism..invertebrates..cytosol.
## 2025-04-09 20:46:21.260034 INFO::Fitting model to feature number 201, P162.PWY..L.glutamate.degradation.V..via.hydroxyglutarate.
## 2025-04-09 20:46:21.26242 INFO::Fitting model to feature number 202, PWY.4041...gamma..glutamyl.cycle
## 2025-04-09 20:46:21.264776 INFO::Fitting model to feature number 203, P108.PWY..pyruvate.fermentation.to.propanoate.I
## 2025-04-09 20:46:21.267183 INFO::Fitting model to feature number 204, PWY.5022..4.aminobutanoate.degradation.V
## 2025-04-09 20:46:21.269567 INFO::Fitting model to feature number 205, GLUDEG.I.PWY..GABA.shunt
## 2025-04-09 20:46:21.272009 INFO::Fitting model to feature number 206, PWY.5677..succinate.fermentation.to.butanoate
## 2025-04-09 20:46:21.274394 INFO::Fitting model to feature number 207, P163.PWY..L.lysine.fermentation.to.acetate.and.butanoate
## 2025-04-09 20:46:21.276797 INFO::Fitting model to feature number 208, PWY.3781..aerobic.respiration.I..cytochrome.c.
## 2025-04-09 20:46:21.279291 INFO::Fitting model to feature number 209, PWY.5083..NAD.NADH.phosphorylation.and.dephosphorylation
## 2025-04-09 20:46:21.281655 INFO::Fitting model to feature number 210, DAPLYSINESYN.PWY..L.lysine.biosynthesis.I
## 2025-04-09 20:46:21.284045 INFO::Fitting model to feature number 211, P461.PWY..hexitol.fermentation.to.lactate..formate..ethanol.and.acetate
## 2025-04-09 20:46:21.286425 INFO::Fitting model to feature number 212, PWY.1861..formaldehyde.assimilation.II..RuMP.Cycle.
## 2025-04-09 20:46:21.288773 INFO::Fitting model to feature number 213, PWY.7312..dTDP.D..beta..fucofuranose.biosynthesis
## 2025-04-09 20:46:21.291197 INFO::Fitting model to feature number 214, PWY.6630..superpathway.of.L.tyrosine.biosynthesis
## 2025-04-09 20:46:21.293567 INFO::Fitting model to feature number 215, PWY.6595..superpathway.of.guanosine.nucleotides.degradation..plants.
## 2025-04-09 20:46:21.295944 INFO::Fitting model to feature number 216, ARG.POLYAMINE.SYN..superpathway.of.arginine.and.polyamine.biosynthesis
## 2025-04-09 20:46:21.298335 INFO::Fitting model to feature number 217, PWY.7003..glycerol.degradation.to.butanol
## 2025-04-09 20:46:21.300735 INFO::Fitting model to feature number 218, P185.PWY..formaldehyde.assimilation.III..dihydroxyacetone.cycle.
## 2025-04-09 20:46:21.303109 INFO::Fitting model to feature number 219, POLYAMSYN.PWY..superpathway.of.polyamine.biosynthesis.I
## 2025-04-09 20:46:21.3055 INFO::Fitting model to feature number 220, PWY0.1298..superpathway.of.pyrimidine.deoxyribonucleosides.degradation
## 2025-04-09 20:46:21.307864 INFO::Fitting model to feature number 221, LACTOSECAT.PWY..lactose.and.galactose.degradation.I
## 2025-04-09 20:46:21.310282 INFO::Fitting model to feature number 222, PWY4LZ.257..superpathway.of.fermentation..Chlamydomonas.reinhardtii.
## 2025-04-09 20:46:21.312631 INFO::Fitting model to feature number 223, P161.PWY..acetylene.degradation
## 2025-04-09 20:46:21.315006 INFO::Fitting model to feature number 224, RUMP.PWY..formaldehyde.oxidation.I
## 2025-04-09 20:46:21.317358 INFO::Fitting model to feature number 225, PPGPPMET.PWY..ppGpp.biosynthesis
## 2025-04-09 20:46:21.319705 INFO::Fitting model to feature number 226, PWY.5304..superpathway.of.sulfur.oxidation..Acidianus.ambivalens.
## 2025-04-09 20:46:21.322095 INFO::Fitting model to feature number 227, PWY.6531..mannitol.cycle
## 2025-04-09 20:46:21.324466 INFO::Fitting model to feature number 228, FUC.RHAMCAT.PWY..superpathway.of.fucose.and.rhamnose.degradation
## 2025-04-09 20:46:21.326827 INFO::Fitting model to feature number 229, PWY.7315..dTDP.N.acetylthomosamine.biosynthesis
## 2025-04-09 20:46:21.329257 INFO::Fitting model to feature number 230, FUCCAT.PWY..fucose.degradation
## 2025-04-09 20:46:21.331647 INFO::Fitting model to feature number 231, PWY.7210..pyrimidine.deoxyribonucleotides.biosynthesis.from.CTP
## 2025-04-09 20:46:21.334101 INFO::Fitting model to feature number 232, FOLSYN.PWY..superpathway.of.tetrahydrofolate.biosynthesis.and.salvage
## 2025-04-09 20:46:21.336505 INFO::Fitting model to feature number 233, PWY.6612..superpathway.of.tetrahydrofolate.biosynthesis
## 2025-04-09 20:46:21.338879 INFO::Fitting model to feature number 234, PWY0.1061..superpathway.of.L.alanine.biosynthesis
## 2025-04-09 20:46:21.341273 INFO::Fitting model to feature number 235, PWY.5189..tetrapyrrole.biosynthesis.II..from.glycine.
## 2025-04-09 20:46:21.343654 INFO::Fitting model to feature number 236, PWY.6876..isopropanol.biosynthesis
## 2025-04-09 20:46:21.346055 INFO::Fitting model to feature number 237, PWY0.781..aspartate.superpathway
## 2025-04-09 20:46:21.348426 INFO::Fitting model to feature number 238, P4.PWY..superpathway.of.L.lysine..L.threonine.and.L.methionine.biosynthesis.I
## 2025-04-09 20:46:21.350792 INFO::Fitting model to feature number 239, PWY0.1479..tRNA.processing
## 2025-04-09 20:46:21.353183 INFO::Fitting model to feature number 240, GLYCOLYSIS.TCA.GLYOX.BYPASS..superpathway.of.glycolysis..pyruvate.dehydrogenase..TCA..and.glyoxylate.bypass
## 2025-04-09 20:46:21.355574 INFO::Fitting model to feature number 241, PYRIDNUCSAL.PWY..NAD.salvage.pathway.I
## 2025-04-09 20:46:21.357929 INFO::Fitting model to feature number 242, GLYCOCAT.PWY..glycogen.degradation.I..bacterial.
## 2025-04-09 20:46:21.360303 INFO::Fitting model to feature number 243, PWY.5723..Rubisco.shunt
## 2025-04-09 20:46:21.362653 INFO::Fitting model to feature number 244, TCA.GLYOX.BYPASS..superpathway.of.glyoxylate.bypass.and.TCA
## 2025-04-09 20:46:21.365054 INFO::Fitting model to feature number 245, PWY.7385..1.3.propanediol.biosynthesis..engineered.
## 2025-04-09 20:46:21.367401 INFO::Fitting model to feature number 246, PWY.7254..TCA.cycle.VII..acetate.producers.
## 2025-04-09 20:46:21.369773 INFO::Fitting model to feature number 247, GLYOXYLATE.BYPASS..glyoxylate.cycle
## 2025-04-09 20:46:21.37216 INFO::Fitting model to feature number 248, PWY.6731..starch.degradation.III
## 2025-04-09 20:46:21.374506 INFO::Fitting model to feature number 249, PWY.7328..superpathway.of.UDP.glucose.derived.O.antigen.building.blocks.biosynthesis
## 2025-04-09 20:46:21.376863 INFO::Fitting model to feature number 250, POLYAMINSYN3.PWY..superpathway.of.polyamine.biosynthesis.II
## 2025-04-09 20:46:21.379247 INFO::Fitting model to feature number 251, PWY.2723..trehalose.degradation.V
## 2025-04-09 20:46:21.38163 INFO::Fitting model to feature number 252, GLUCOSE1PMETAB.PWY..glucose.and.glucose.1.phosphate.degradation
## 2025-04-09 20:46:21.384017 INFO::Fitting model to feature number 253, PWY.5384..sucrose.degradation.IV..sucrose.phosphorylase.
## 2025-04-09 20:46:21.386396 INFO::Fitting model to feature number 254, PWY.7046..4.coumarate.degradation..anaerobic.
## 2025-04-09 20:46:21.388776 INFO::Fitting model to feature number 255, PWY66.389..phytol.degradation
## 2025-04-09 20:46:21.391161 INFO::Fitting model to feature number 256, PWY.5971..palmitate.biosynthesis.II..bacteria.and.plants.
## 2025-04-09 20:46:21.393536 INFO::Fitting model to feature number 257, PWY.6629..superpathway.of.L.tryptophan.biosynthesis
## 2025-04-09 20:46:21.3959 INFO::Fitting model to feature number 258, PWY.5345..superpathway.of.L.methionine.biosynthesis..by.sulfhydrylation.
## 2025-04-09 20:46:21.398272 INFO::Fitting model to feature number 259, SULFATE.CYS.PWY..superpathway.of.sulfate.assimilation.and.cysteine.biosynthesis
## 2025-04-09 20:46:21.40066 INFO::Fitting model to feature number 260, PWY.5838..superpathway.of.menaquinol.8.biosynthesis.I
## 2025-04-09 20:46:21.403071 INFO::Fitting model to feature number 261, PRPP.PWY..superpathway.of.histidine..purine..and.pyrimidine.biosynthesis
## 2025-04-09 20:46:21.405442 INFO::Fitting model to feature number 262, PWY.5845..superpathway.of.menaquinol.9.biosynthesis
## 2025-04-09 20:46:21.407808 INFO::Fitting model to feature number 263, PWY.6113..superpathway.of.mycolate.biosynthesis
## 2025-04-09 20:46:21.434808 INFO::Fitting model to feature number 264, PWY.5897..superpathway.of.menaquinol.11.biosynthesis
## 2025-04-09 20:46:21.437204 INFO::Fitting model to feature number 265, PWY.5898..superpathway.of.menaquinol.12.biosynthesis
## 2025-04-09 20:46:21.439515 INFO::Fitting model to feature number 266, PWY.5899..superpathway.of.menaquinol.13.biosynthesis
## 2025-04-09 20:46:21.441842 INFO::Fitting model to feature number 267, PWY.7117..C4.photosynthetic.carbon.assimilation.cycle..PEPCK.type
## 2025-04-09 20:46:21.444324 INFO::Fitting model to feature number 268, PWY.6969..TCA.cycle.V..2.oxoglutarate.ferredoxin.oxidoreductase.
## 2025-04-09 20:46:21.446646 INFO::Fitting model to feature number 269, PWY.6628..superpathway.of.L.phenylalanine.biosynthesis
## 2025-04-09 20:46:21.448998 INFO::Fitting model to feature number 270, PWY.5861..superpathway.of.demethylmenaquinol.8.biosynthesis
## 2025-04-09 20:46:21.451344 INFO::Fitting model to feature number 271, PWY.5862..superpathway.of.demethylmenaquinol.9.biosynthesis
## 2025-04-09 20:46:21.453684 INFO::Fitting model to feature number 272, FERMENTATION.PWY..mixed.acid.fermentation
## 2025-04-09 20:46:21.456053 INFO::Fitting model to feature number 273, PWY.241..C4.photosynthetic.carbon.assimilation.cycle..NADP.ME.type
## 2025-04-09 20:46:21.458414 INFO::Fitting model to feature number 274, SO4ASSIM.PWY..sulfate.reduction.I..assimilatory.
## 2025-04-09 20:46:21.460763 INFO::Fitting model to feature number 275, KETOGLUCONMET.PWY..ketogluconate.metabolism
## 2025-04-09 20:46:21.463159 INFO::Fitting model to feature number 276, PWY.5840..superpathway.of.menaquinol.7.biosynthesis
## 2025-04-09 20:46:21.465701 INFO::Fitting model to feature number 277, PWY.5850..superpathway.of.menaquinol.6.biosynthesis.I
## 2025-04-09 20:46:21.468076 INFO::Fitting model to feature number 278, PWY.5896..superpathway.of.menaquinol.10.biosynthesis
## 2025-04-09 20:46:21.470431 INFO::Fitting model to feature number 279, P105.PWY..TCA.cycle.IV..2.oxoglutarate.decarboxylase.
## 2025-04-09 20:46:21.472798 INFO::Fitting model to feature number 280, PWY.5913..TCA.cycle.VI..obligate.autotrophs.
## 2025-04-09 20:46:21.475198 INFO::Fitting model to feature number 281, PWY.561..superpathway.of.glyoxylate.cycle.and.fatty.acid.degradation
## 2025-04-09 20:46:21.477564 INFO::Fitting model to feature number 282, PWY.4702..phytate.degradation.I
## 2025-04-09 20:46:21.479898 INFO::Fitting model to feature number 283, PWY.6803..phosphatidylcholine.acyl.editing
## 2025-04-09 20:46:21.482323 INFO::Fitting model to feature number 284, PWY.7115..C4.photosynthetic.carbon.assimilation.cycle..NAD.ME.type
## 2025-04-09 20:46:21.484673 INFO::Fitting model to feature number 285, PWY.5918..superpathay.of.heme.biosynthesis.from.glutamate
## 2025-04-09 20:46:21.487047 INFO::Fitting model to feature number 286, PWY.7234..inosine.5..phosphate.biosynthesis.III
## 2025-04-09 20:46:21.489396 INFO::Fitting model to feature number 287, PWY.6285..superpathway.of.fatty.acids.biosynthesis..E..coli.
## 2025-04-09 20:46:21.49177 INFO::Fitting model to feature number 288, PWY.5860..superpathway.of.demethylmenaquinol.6.biosynthesis.I
## 2025-04-09 20:46:21.49416 INFO::Fitting model to feature number 289, PWY.5863..superpathway.of.phylloquinol.biosynthesis
## 2025-04-09 20:46:21.496588 INFO::Fitting model to feature number 290, HEME.BIOSYNTHESIS.II..heme.biosynthesis.I..aerobic.
## 2025-04-09 20:46:21.499604 INFO::Fitting model to feature number 291, PWY.821..superpathway.of.sulfur.amino.acid.biosynthesis..Saccharomyces.cerevisiae.
## 2025-04-09 20:46:21.502057 INFO::Fitting model to feature number 292, PWY.5675..nitrate.reduction.V..assimilatory.
## 2025-04-09 20:46:21.504427 INFO::Fitting model to feature number 293, PWY.5791..1.4.dihydroxy.2.naphthoate.biosynthesis.II..plants.
## 2025-04-09 20:46:21.506818 INFO::Fitting model to feature number 294, PWY.5837..1.4.dihydroxy.2.naphthoate.biosynthesis.I
## 2025-04-09 20:46:21.509186 INFO::Fitting model to feature number 295, PWY.5920..superpathway.of.heme.biosynthesis.from.glycine
## 2025-04-09 20:46:21.511524 INFO::Fitting model to feature number 296, PWY.7204..pyridoxal.5..phosphate.salvage.II..plants.
## 2025-04-09 20:46:21.513868 INFO::Fitting model to feature number 297, ENTBACSYN.PWY..enterobactin.biosynthesis
## 2025-04-09 20:46:21.51624 INFO::Fitting model to feature number 298, PWY0.1415..superpathway.of.heme.biosynthesis.from.uroporphyrinogen.III
## 2025-04-09 20:46:21.518587 INFO::Fitting model to feature number 299, HEMESYN2.PWY..heme.biosynthesis.II..anaerobic.
## 2025-04-09 20:46:21.520922 INFO::Fitting model to feature number 300, PWY.6284..superpathway.of.unsaturated.fatty.acids.biosynthesis..E..coli.
## 2025-04-09 20:46:21.523293 INFO::Fitting model to feature number 301, P42.PWY..incomplete.reductive.TCA.cycle
## 2025-04-09 20:46:21.525649 INFO::Fitting model to feature number 302, PWY.5656..mannosylglycerate.biosynthesis.I
## 2025-04-09 20:46:21.528025 INFO::Fitting model to feature number 303, PWY.5173..superpathway.of.acetyl.CoA.biosynthesis
## 2025-04-09 20:46:21.530366 INFO::Fitting model to feature number 304, ECASYN.PWY..enterobacterial.common.antigen.biosynthesis
## 2025-04-09 20:46:21.532714 INFO::Fitting model to feature number 305, AST.PWY..L.arginine.degradation.II..AST.pathway.
## 2025-04-09 20:46:21.535119 INFO::Fitting model to feature number 306, PWY3O.355..stearate.biosynthesis.III..fungi.
## 2025-04-09 20:46:21.537509 INFO::Fitting model to feature number 307, PWY0.42..2.methylcitrate.cycle.I
## 2025-04-09 20:46:21.539892 INFO::Fitting model to feature number 308, PWY.7094..fatty.acid.salvage
## 2025-04-09 20:46:21.542293 INFO::Fitting model to feature number 309, PWY.5747..2.methylcitrate.cycle.II
## 2025-04-09 20:46:21.544661 INFO::Fitting model to feature number 310, PWY.5367..petroselinate.biosynthesis
## 2025-04-09 20:46:21.547032 INFO::Fitting model to feature number 311, PWY0.1533..methylphosphonate.degradation.I
## 2025-04-09 20:46:21.54937 INFO::Fitting model to feature number 312, PWY.6823..molybdenum.cofactor.biosynthesis
## 2025-04-09 20:46:21.551721 INFO::Fitting model to feature number 313, PWY.5705..allantoin.degradation.to.glyoxylate.III
## 2025-04-09 20:46:21.554097 INFO::Fitting model to feature number 314, LPSSYN.PWY..superpathway.of.lipopolysaccharide.biosynthesis
## 2025-04-09 20:46:21.556528 INFO::Fitting model to feature number 315, REDCITCYC..TCA.cycle.VIII..helicobacter.
## 2025-04-09 20:46:21.558867 INFO::Fitting model to feature number 316, GLYCOL.GLYOXDEG.PWY..superpathway.of.glycol.metabolism.and.degradation
## 2025-04-09 20:46:21.561252 INFO::Fitting model to feature number 317, P122.PWY..heterolactic.fermentation
## 2025-04-09 20:46:21.563631 INFO::Fitting model to feature number 318, KDO.NAGLIPASYN.PWY..superpathway.of..Kdo.2.lipid.A.biosynthesis
## 2025-04-09 20:46:21.565998 INFO::Fitting model to feature number 319, PWY.7446..sulfoglycolysis
## 2025-04-09 20:46:21.568353 INFO::Fitting model to feature number 320, PWY490.3..nitrate.reduction.VI..assimilatory.
## 2025-04-09 20:46:21.570694 INFO::Fitting model to feature number 321, PWY.7209..superpathway.of.pyrimidine.ribonucleosides.degradation
## 2025-04-09 20:46:21.573064 INFO::Fitting model to feature number 322, UBISYN.PWY..superpathway.of.ubiquinol.8.biosynthesis..prokaryotic.
## 2025-04-09 20:46:21.575427 INFO::Fitting model to feature number 323, PWY0.41..allantoin.degradation.IV..anaerobic.
## 2025-04-09 20:46:21.577772 INFO::Fitting model to feature number 324, PWY.5855..ubiquinol.7.biosynthesis..prokaryotic.
## 2025-04-09 20:46:21.580138 INFO::Fitting model to feature number 325, PWY.5856..ubiquinol.9.biosynthesis..prokaryotic.
## 2025-04-09 20:46:21.582482 INFO::Fitting model to feature number 326, PWY.5857..ubiquinol.10.biosynthesis..prokaryotic.
## 2025-04-09 20:46:21.584857 INFO::Fitting model to feature number 327, PWY.6708..ubiquinol.8.biosynthesis..prokaryotic.
## 2025-04-09 20:46:21.58722 INFO::Fitting model to feature number 328, PWY.5692..allantoin.degradation.to.glyoxylate.II
## 2025-04-09 20:46:21.589558 INFO::Fitting model to feature number 329, URDEGR.PWY..superpathway.of.allantoin.degradation.in.plants
## 2025-04-09 20:46:21.591908 INFO::Fitting model to feature number 330, PWY0.1338..polymyxin.resistance
## 2025-04-09 20:46:21.594272 INFO::Fitting model to feature number 331, P221.PWY..octane.oxidation
## 2025-04-09 20:46:21.596616 INFO::Fitting model to feature number 332, THREOCAT.PWY..superpathway.of.L.threonine.metabolism
## 2025-04-09 20:46:21.598948 INFO::Fitting model to feature number 333, NONMEVIPP.PWY..methylerythritol.phosphate.pathway.I
## 2025-04-09 20:46:21.60132 INFO::Fitting model to feature number 334, PWY.7560..methylerythritol.phosphate.pathway.II
## 2025-04-09 20:46:21.603642 INFO::Fitting model to feature number 335, PWY.5121..superpathway.of.geranylgeranyl.diphosphate.biosynthesis.II..via.MEP.
## 2025-04-09 20:46:21.606014 INFO::Fitting model to feature number 336, PWY.7392..taxadiene.biosynthesis..engineered.
## 2025-04-09 20:46:21.608359 INFO::Fitting model to feature number 337, PWY.6143..CMP.pseudaminate.biosynthesis
## 2025-04-09 20:46:21.610722 INFO::Fitting model to feature number 338, PWY.6270..isoprene.biosynthesis.I
## 2025-04-09 20:46:21.613073 INFO::Fitting model to feature number 339, ALLANTOINDEG.PWY..superpathway.of.allantoin.degradation.in.yeast
## 2025-04-09 20:46:21.615431 INFO::Fitting model to feature number 340, PWY.6263..superpathway.of.menaquinol.8.biosynthesis.II
## 2025-04-09 20:46:21.617774 INFO::Fitting model to feature number 341, PWY.7371..1.4.dihydroxy.6.naphthoate.biosynthesis.II
## 2025-04-09 20:46:21.620144 INFO::Fitting model to feature number 342, ARGORNPROST.PWY..arginine..ornithine.and.proline.interconversion
## 2025-04-09 20:46:21.622493 INFO::Fitting model to feature number 343, PWY66.398..TCA.cycle.III..animals.
## 2025-04-09 20:46:21.624837 INFO::Fitting model to feature number 344, PWY.5464..superpathway.of.cytosolic.glycolysis..plants...pyruvate.dehydrogenase.and.TCA.cycle
## 2025-04-09 20:46:21.627211 INFO::Fitting model to feature number 345, ORNDEG.PWY..superpathway.of.ornithine.degradation
## 2025-04-09 20:46:21.629549 INFO::Fitting model to feature number 346, P23.PWY..reductive.TCA.cycle.I
## 2025-04-09 20:46:21.631926 INFO::Fitting model to feature number 347, PWY0.1277..3.phenylpropanoate.and.3..3.hydroxyphenyl.propanoate.degradation
## 2025-04-09 20:46:21.634344 INFO::Fitting model to feature number 348, ARGDEG.PWY..superpathway.of.L.arginine..putrescine..and.4.aminobutanoate.degradation
## 2025-04-09 20:46:21.636693 INFO::Fitting model to feature number 349, ORNARGDEG.PWY..superpathway.of.L.arginine.and.L.ornithine.degradation
## 2025-04-09 20:46:21.639054 INFO::Fitting model to feature number 350, HCAMHPDEG.PWY..3.phenylpropanoate.and.3..3.hydroxyphenyl.propanoate.degradation.to.2.oxopent.4.enoate
## 2025-04-09 20:46:21.641393 INFO::Fitting model to feature number 351, PWY.6690..cinnamate.and.3.hydroxycinnamate.degradation.to.2.oxopent.4.enoate
## 2025-04-09 20:46:21.643862 INFO::Fitting model to feature number 352, PROTOCATECHUATE.ORTHO.CLEAVAGE.PWY..protocatechuate.degradation.II..ortho.cleavage.pathway.
## 2025-04-09 20:46:21.646239 INFO::Fitting model to feature number 353, P124.PWY..Bifidobacterium.shunt
## 2025-04-09 20:46:21.648575 INFO::Fitting model to feature number 354, PWY.622..starch.biosynthesis
## 2025-04-09 20:46:21.650901 INFO::Fitting model to feature number 355, PWY.7269..NAD.NADP.NADH.NADPH.mitochondrial.interconversion..yeast.
## 2025-04-09 20:46:21.653253 INFO::Fitting model to feature number 356, PWY.7316..dTDP.N.acetylviosamine.biosynthesis
## 2025-04-09 20:46:21.655595 INFO::Fitting model to feature number 357, PWY.7279..aerobic.respiration.II..cytochrome.c...yeast.
## 2025-04-09 20:46:21.657913 INFO::Fitting model to feature number 358, PWY.6837..fatty.acid.beta.oxidation.V..unsaturated..odd.number..di.isomerase.dependent.
## 2025-04-09 20:46:21.660257 INFO::Fitting model to feature number 359, X3.HYDROXYPHENYLACETATE.DEGRADATION.PWY..4.hydroxyphenylacetate.degradation
## 2025-04-09 20:46:21.66259 INFO::Fitting model to feature number 360, PWY.6953..dTDP.3.acetamido.3.6.dideoxy..alpha..D.galactose.biosynthesis
## 2025-04-09 20:46:21.664923 INFO::Fitting model to feature number 361, PWY.7616..methanol.oxidation.to.carbon.dioxide
## 2025-04-09 20:46:21.66727 INFO::Fitting model to feature number 362, PWY.5088..L.glutamate.degradation.VIII..to.propanoate.
## 2025-04-09 20:46:21.669609 INFO::Fitting model to feature number 363, PWY0.881..superpathway.of.fatty.acid.biosynthesis.I..E..coli.
## 2025-04-09 20:46:21.720517 INFO::Counting total values for each feature
## 2025-04-09 20:46:21.750772 INFO::Writing filtered data to file output_pwys/features/filtered_data.tsv
## 2025-04-09 20:46:21.77907 INFO::Writing filtered, normalized data to file output_pwys/features/filtered_data_norm.tsv
## 2025-04-09 20:46:21.807067 INFO::Writing filtered, normalized, transformed data to file output_pwys/features/filtered_data_norm_transformed.tsv
## 2025-04-09 20:46:21.843437 INFO::Writing residuals to file output_pwys/fits/residuals.rds
## 2025-04-09 20:46:21.864721 INFO::Writing fitted values to file output_pwys/fits/fitted.rds
## 2025-04-09 20:46:21.879068 INFO::Writing all results to file (ordered by increasing q-values): output_pwys/all_results.tsv
## 2025-04-09 20:46:21.883705 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
## 2025-04-09 20:46:21.884486 INFO::Writing heatmap of significant results to file: output_pwys/heatmap.pdf
## [1] "There are no associations to plot!"
## 2025-04-09 20:46:21.885434 INFO::Writing association plots (one for each significant association) to output folder: output_pwys
## 2025-04-09 20:46:21.888779 INFO::Plotting associations from most to least significant, grouped by metadata
## 2025-04-09 20:46:21.889361 INFO::Plotting data for metadata number 1, antibiotics_current_use
## 2025-04-09 20:46:21.890461 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"