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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod318

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod318 Module size 36 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 53947 A4GALT alpha 1,4-galactosyltransferase (P blood group) 2515 ADAM2 ADAM metallopeptidase domain 2 8748 ADAM20 ADAM metallopeptidase domain 20 8747 ADAM21 ADAM metallopeptidase domain 21 11085 ADAM30 ADAM metallopeptidase domain 30 175 AGA aspartylglucosaminidase 80150 ASRGL1 asparaginase like 1 8706 B3GALNT1 beta-1,3-N-acetylgalactosaminyltransferase 1 (globoside blood group) 2583 B4GALNT1 beta-1,4-N-acetyl-galactosaminyltransferase 1 9331 B4GALT6 beta-1,4-galactosyltransferase 6 1116 CHI3L1 chitinase 3 like 1 1117 CHI3L2 chitinase 3 like 2 27159 CHIA chitinase, acidic 1118 CHIT1 chitinase 1 1476 CST6 cystatin B 51076 CUTC cutC copper transporter 64772 ENGASE endo-beta-N-acetylglucosaminidase 2517 FUCA1 alpha-L-fucosidase 1 2519 FUCA2 alpha-L-fucosidase 2 2530 FUT8 fucosyltransferase 8 2720 GLB1 galactosidase beta 1 2760 GM2A GM2 ganglioside activator 3073 HEXA hexosaminidase subunit alpha 3074 HEXB hexosaminidase subunit beta 3906 LALBA lactalbumin alpha 3938 LCT lactase 4668 NAGA alpha-N-acetylgalactosaminidase 55577 NAGK N-acetylglucosamine kinase 5016 OVGP1 oviductal glycoprotein 1 124912 SPACA3 sperm acrosome associated 3 8869 ST3GAL5 ST3 beta-galactoside alpha-2,3-sialyltransferase 5 84302 TMEM246 transmembrane protein 246 57829 ZP1 zona pellucida glycoprotein 4 7783 ZP2 zona pellucida glycoprotein 2 7784 ZP3 zona pellucida glycoprotein 3 57829 ZP4 zona pellucida glycoprotein 4

Functional annotation

Modules were tested for enrichment in functional and pathway annotations using two complementary approaches:
1. To select a small number of specific / non-redundant annotations for each module, a regression-based approach was used;
2. To obtain the complete set of enriched annotations, an extension of Fisher’s exact test that takes annotation bias into account was employed (Wallenius’ non-central hypergeometric distribution).

Most specific annotations for this module

Coeff.1 P-value.2 Source.3 Term.4 Class.5 6.25e-01 1.97e-24 Reactome Interaction With The Zona Pellucida Reproduction 2.81e-01 1.21e-05 GO beta-N-acetylhexosaminidase activity molecular_function 2.42e-01 1.56e-13 GO chitin binding molecular_function 1.86e-01 2.70e-07 GO glycoside catabolic process biological_process 1.47e-01 1.56e-13 GO chitin catabolic process biological_process 1.46e-01 1.56e-13 GO chitinase activity molecular_function 4.18e-02 5.88e-11 GO glycosphingolipid metabolic process biological_process 3.46e-02 1.44e-04 GO glycosphingolipid biosynthetic process biological_process 3.07e-02 8.42e-05 GO fucose metabolic process biological_process 3.02e-02 1.80e-04 GO protein deglycosylation biological_process 2.50e-02 9.21e-07 Reactome Digestion of dietary carbohydrate Digestion and absorption 2.24e-02 1.44e-04 GO ganglioside biosynthetic process biological_process 2.09e-02 1.68e-06 GO keratan sulfate catabolic process biological_process 1.92e-02 1.68e-06 Reactome Keratan sulfate degradation Metabolism 1.15e-02 7.34e-06 GO lipid storage biological_process 5.75e-03 1.80e-04 Reactome Reactions specific to the complex N-glycan synthesis pathway Metabolism of proteins

¹Regression coefficient

²Fisher’s exact test nominal P-value

³Annotation source (Reactome, GO biological process (BP), molecular function (MF) and cellular component (CC))

⁴GO category or Reactome pathway

⁵High-level branch of annotation tree

Gene membership

All enriched annotations

Gene Ontology

P-value1 FDR2 Term 0.00e+00 0.00e+00 binding of sperm to zona pellucida 0.00e+00 0.00e+00 sperm-egg recognition 0.00e+00 0.00e+00 cell recognition 0.00e+00 0.00e+00 fertilization 0.00e+00 0.00e+00 single fertilization 0.00e+00 0.00e+00 cell-cell recognition 0.00e+00 0.00e+00 carbohydrate metabolic process 0.00e+00 0.00e+00 glycolipid metabolic process 0.00e+00 0.00e+00 glycosphingolipid metabolic process 0.00e+00 0.00e+00 hydrolase activity, hydrolyzing O-glycosyl compounds 0.00e+00 0.00e+00 hydrolase activity, acting on glycosyl bonds 5.92e-12 5.37e-09 chitin catabolic process 5.92e-12 5.37e-09 chitin metabolic process 1.85e-11 1.20e-08 chitinase activity 5.19e-10 3.99e-07 membrane lipid metabolic process 8.96e-10 6.71e-07 amino sugar metabolic process 1.59e-09 1.15e-06 sphingolipid metabolic process 2.08e-09 1.05e-06 chitin binding 9.08e-09 5.93e-06 oligosaccharide metabolic process 1.94e-08 7.39e-06 secretory granule

¹1Nominal enrichment p-value (Wallenius’ noncentral hypergeometric distribution)

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 1.29e-08 2.79e-06 GLYCOSPHINGOLIPID METABOLISM 1.33e-07 2.55e-05 SPHINGOLIPID METABOLISM 1.37e-07 2.62e-05 KERATAN SULFATE KERATIN METABOLISM 2.29e-07 4.29e-05 KERATAN SULFATE DEGRADATION 3.27e-07 7.88e-05 KERATAN SULFATE KERATIN METABOLISM 4.78e-07 1.13e-04 GLYCOSPHINGOLIPID METABOLISM 1.54e-06 3.37e-04 KERATAN SULFATE DEGRADATION 3.32e-06 6.85e-04 SPHINGOLIPID METABOLISM 1.17e-05 2.21e-03 METABOLISM OF CARBOHYDRATES 1.19e-05 1.75e-03 METABOLISM OF CARBOHYDRATES 2.02e-05 2.89e-03 GLYCOSAMINOGLYCAN METABOLISM 2.25e-05 4.03e-03 GLYCOSAMINOGLYCAN METABOLISM 4.01e-05 5.46e-03 PHOSPHOLIPID METABOLISM 1.13e-04 1.42e-02 HYALURONAN UPTAKE AND DEGRADATION 1.73e-04 2.53e-02 PHOSPHOLIPID METABOLISM 1.80e-04 2.16e-02 HYALURONAN METABOLISM 3.70e-04 4.93e-02 CS DS DEGRADATION 4.05e-04 4.49e-02 CS DS DEGRADATION 4.31e-04 5.65e-02 N GLYCAN ANTENNAE ELONGATION IN THE MEDIAL TRANS GOLGI 4.42e-04 5.78e-02 HYALURONAN UPTAKE AND DEGRADATION

¹1Nominal enrichment p-value (Wallenius’ noncentral hypergeometric distribution)

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 1.19e-07 1.60e-03 thin zona pellucida 4.77e-05 1.38e-01 abnormal cumulus oophorus 7.16e-05 1.81e-01 Purkinje cell degeneration 2.17e-04 3.66e-01 abnormal secondary ovarian follicle morphology 7.17e-04 7.46e-01 abnormal neuron morphology 7.43e-04 7.62e-01 abnormal hepatocyte morphology 7.59e-04 7.66e-01 abnormal ovulation 1.60e-03 1.00e+00 abnormal ovarian folliculogenesis 1.62e-03 1.00e+00 abnormal nervous system physiology 1.87e-03 1.00e+00 abnormal limbic system morphology 1.91e-03 1.00e+00 abnormal epididymis morphology 2.38e-03 1.00e+00 abnormal brain morphology 3.74e-03 1.00e+00 abnormal kidney calyx morphology 5.61e-03 1.00e+00 abnormal entorhinal cortex morphology 5.61e-03 1.00e+00 neurogenic bladder 5.61e-03 1.00e+00 abnormal efferent ductules of testis morphology 5.62e-03 1.00e+00 multifocal hepatic necrosis 5.83e-03 1.00e+00 ataxia 7.48e-03 1.00e+00 orthokeratosis 9.33e-03 1.00e+00 increased total lung capacity

¹1Nominal enrichment p-value (Wallenius’ noncentral hypergeometric distribution)

²FDR corrected p-value (Benjamini-Hochberg)