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KEGG MODULE specifications


Unique identifier OMICS_21134
Restrictions to use None
Community driven No
Data access Browse
User data submission Not allowed
Maintained Yes


  • person_outline Kae Morishima

Publication for KEGG MODULE

KEGG MODULE citations


Multi omics differentially classify disease state and treatment outcome in pediatric Crohn’s disease

PMCID: 5769311
PMID: 29335008
DOI: 10.1186/s40168-018-0398-3

[…] thin each sample by the median universal single-copy gene abundance, which controls for inter-sample variation in microbial genome sizes. We then ran HUMAnN2 on these normalized values to reconstruct KEGG module and pathway abundances within each sample. No taxa or functions were identified in the MGS of two samples, S34 and S38 (16S sequencing also failed for these samples, see below), which were […]


Machine Learning Leveraging Genomes from Metagenomes Identifies Influential Antibiotic Resistance Genes in the Infant Gut Microbiome

PMCID: 5758725
PMID: 29359195
DOI: 10.1128/mSystems.00123-17

[…] oto Encyclopedia of Genes and Genomes (KEGG) () HMMs and the results were parsed for genome profiling. This resulted in a KEGG metabolism profile for each organism that displayed the fraction of each KEGG module encoded by that genome (). […]


The Plasticizer Bisphenol A Perturbs the Hepatic Epigenome: A Systems Level Analysis of the miRNome

PMCID: 5664119
PMID: 29027980
DOI: 10.3390/genes8100269

[…] mic functions is captured from literature and organized in the following forms: [i] Pathway map—in KEGG PATHWAY; [ii] Brite hierarchy and table—in KEGG BRITE; [iii] Membership (logical expression)—in KEGG MODULE; and [iv] Membership (simple list)—in KEGG DISEASE. […]


Methyl donor deficient diets cause distinct alterations in lipid metabolism but are poorly representative of human NAFLD

Wellcome Open Res
PMCID: 5887079
PMID: 29707653
DOI: 10.21956/wellcomeopenres.13206.r25266

[…] ackage ( Investigation of fat handling was performed by interrogating relevant pathways of lipid metabolism and insulin signalling from the Kyoto encyclopedia for genes and genomes (KEGG) module database ( KEGG module sets ‘M00003 gluconeogenesis’, ‘M00086 beta-Oxidation, acyl-CoA synthesis’, ‘M00083 Fatty acid biosynthesis, elongation’ and […]


Fluoride Depletes Acidogenic Taxa in Oral but Not Gut Microbial Communities in Mice

PMCID: 5547758
PMID: 28808691
DOI: 10.1128/mSystems.00047-17

[…] rved functional modules were differentially abundant among the treatment groups (). Fluoride treatment was associated with depletions in the glyoxylate cycle (Kyoto Encyclopedia of Genes and Genomes [KEGG] module M00012), succinate dehydrogenase (KEGG module M00149), and second-carbon oxidation (KEGG module M00311) reflecting perturbed central carbon metabolism (). In addition, depletion in the me […]


Molecular Characterization of the Human Stomach Microbiota in Gastric Cancer Patients

PMCID: 5498480
PMID: 28730144
DOI: 10.3389/fcimb.2017.00302

[…] r to compare gastric microbiota with the oral, nasal, stool, skin, and vagina microbiota from the HMP study, we calculated Euclidean/Bray-Curtis distances and generated a matrix from the phylum-level/KEGG module profiles, performed principal coordinate analysis (PCoA) on the Euclidean/Bray-Curtis distance matrix, and then plotted the figure based on the first three principal coordinates to visuali […]


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KEGG MODULE institution(s)
Bioinformatics Center, Institute for Chemical Research, Kyoto University, Kyoto, Japan; Human Genome Center, Institute of Medical Science, University of Tokyo, Tokyo, Japan; Life Science Solutions Department, Fujitsu Kyushu Systems Ltd., Fukuoka, Japan
KEGG MODULE funding source(s)
Supported by Japan Science and Technology Agency (KEGG project, partial); Bioinformatics Center, Institute for Chemical Research, Kyoto University (computational resource).


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