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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod311

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod311 Module size 79 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 23780 APOL2 apolipoprotein L2 460 ASTN1 astrotactin 1 11118 BTN3A2 butyrophilin subfamily 3 member A2 119032 C10orf32 BLOC-1 related complex subunit 7 79591 C10orf76 armadillo-like helical domain containing 3 80007 C10orf88 chromosome 10 open reading frame 88 79703 C11orf80 chromosome 11 open reading frame 80 28974 C19orf53 chromosome 19 open reading frame 53 374920 C19orf68 zinc finger SWIM-type containing 9 339512 C1orf110 coiled-coil domain containing 190 25912 C1orf43 chromosome 1 open reading frame 43 130355 C2orf76 chromosome 2 open reading frame 76 285679 C5orf60 chromosome 5 open reading frame 60 114926 C8orf40 small integral membrane protein 19 79714 CCDC51 coiled-coil domain containing 51 100529251 CKLF-CMTM1 CKLF-CMTM1 readthrough 23155 CLCC1 chloride channel CLIC like 1 79974 CPED1 cadherin like and PC-esterase domain containing 1 404217 CTXN1 cortexin 1 285761 DCBLD1 discoidin, CUB and LCCL domain containing 1 10311 DSCR3 VPS26 endosomal protein sorting factor C 56986 DTWD1 DTW domain containing 1 114794 ELFN2 extracellular leucine rich repeat and fibronectin type III domain containing 2 57724 EPG5 ectopic P-granules autophagy protein 5 homolog 84141 EVA1A eva-1 homolog A, regulator of programmed cell death 728118 FAM22A NUT family member 2A 54537 FAM35A shieldin complex subunit 2 163933 FAM43B family with sequence similarity 43 member B 654463 FER1L6 fer-1 like family member 6 170575 GIMAP1 GTPase, IMAP family member 1 313771 GLTP ceramide-1-phosphate transfer protein 647042 GOLGA6L10 golgin A6 family-like 10 728498 GOLGA8H golgin A8 family member H 151556 GPR155 G protein-coupled receptor 155 79807 GSTCD glutathione S-transferase C-terminal domain containing 387597 ILDR2 immunoglobulin like domain containing receptor 2 57528 KCTD16 potassium channel tetramerization domain containing 16 9786 KIAA0586 KIAA0586 57691 KIAA1586 KIAA1586 196374 KRT78 keratin 78 10184 LHFPL2 LHFPL tetraspan subfamily member 2 7798 LUZP1 leucine zipper protein 1 54742 LY6K lymphocyte antigen 6 family member K 91862 MARVELD3 MARVEL domain containing 3 55784 MCTP2 multiple C2 and transmembrane domain containing 2 79710 MORC4 MORC family CW-type zinc finger 4 139221 MUM1L1 MUM1 like 1 347273 MURC caveolae associated protein 4 204801 NLRP11 NLR family pyrin domain containing 11 126204 NLRP13 NLR family pyrin domain containing 13 169611 OLFML2A olfactomedin like 2A 286530 P2RY8 P2Y receptor family member 8 7262 PHLDA2 pleckstrin homology like domain family A member 2 653583 PHLDB3 pleckstrin homology like domain family B member 3 10464 PIBF1 progesterone immunomodulatory binding factor 1 79990 PLEKHH3 pleckstrin homology, MyTH4 and FERM domain containing H3 391004 PRAMEF17 PRAME family member 17 401399 PRRT4 proline rich transmembrane protein 4 92241 RCSD1 RCSD domain containing 1 285671 RNF180 ring finger protein 180 146923 RUNDC1 RUN domain containing 1 122060 SLAIN1 SLAIN motif family member 1 51310 SLC22A17 solute carrier family 22 member 17 28231 SLCO4A1 solute carrier organic anion transporter family member 4A1 79925 SPEF2 sperm flagellar 2 153218 SPINK13 serine peptidase inhibitor, Kazal type 13 (putative) 26032 SUSD5 sushi domain containing 5 9144 SYNGR2 synaptogyrin 2 54929 TMEM161A transmembrane protein 161A 92703 TMEM183A transmembrane protein 183A 387890 TMEM233 transmembrane protein 233 55219 TMEM57 macoilin 1 147166 TRIM16L tripartite motif containing 16 like 286144 TRIQK triple QxxK/R motif containing 55761 TTC17 tetratricopeptide repeat domain 17 100134938 UPK3BL uroplakin 3B like 1 9605 VPS9D1 VPS9 domain containing 1 54838 WBP1L WW domain binding protein 1 like 90199 WFDC8 WAP four-disulfide core domain 8

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).

No specific annotations were found for this module

All enriched annotations

Gene Ontology

P-value1 FDR2 Term 1.95e-03 3.34e-01 neural fold formation 1.95e-03 3.34e-01 regulation of natural killer cell activation 1.95e-03 3.34e-01 negative regulation of natural killer cell activation 2.16e-03 3.62e-01 response to osmotic stress 2.95e-03 4.66e-01 hormone transport 3.90e-03 5.71e-01 morphogenesis of an epithelial fold 3.90e-03 5.71e-01 activation of Janus kinase activity 3.90e-03 5.71e-01 negative regulation of fatty acid biosynthetic process 4.86e-03 5.99e-01 SUMO ligase activity 5.32e-03 6.45e-01 mitogen-activated protein kinase kinase kinase binding 5.84e-03 7.72e-01 siderophore transport 5.84e-03 7.72e-01 norepinephrine metabolic process 6.06e-03 7.18e-01 interleukin-4 receptor binding 6.62e-03 7.73e-01 oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced ascorbate as one donor, and incorporation of one atom of oxygen 7.78e-03 9.47e-01 cellular hyperosmotic response 7.78e-03 9.47e-01 serotonin metabolic process 7.78e-03 9.47e-01 interferon-gamma secretion 7.78e-03 9.47e-01 negative regulation of interleukin-12 production 8.64e-03 1.00e+00 negative regulation of intracellular signal transduction 9.70e-03 1.00e+00 glycolipid transporter activity

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 6.04e-03 5.35e-01 TRANSPORT OF ORGANIC ANIONS 9.66e-03 7.80e-01 TRANSPORT OF VITAMINS NUCLEOSIDES AND RELATED MOLECULES

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 1.87e-03 1e+00 abnormal roof plate morphology 1.87e-03 1e+00 axonal spheroids 3.74e-03 1e+00 increased hindbrain apoptosis 3.74e-03 1e+00 abnormal lateral nasal prominence morphology 3.74e-03 1e+00 abnormal medial nasal prominence morphology 3.74e-03 1e+00 decreased cerebral cortex pyramidal cell number 3.74e-03 1e+00 decreased white fat cell lipid droplet size 5.61e-03 1e+00 abnormal neural fold morphology 5.61e-03 1e+00 abnormal perineum morphology 5.61e-03 1e+00 abnormal vagina morphology 5.61e-03 1e+00 narrow head 5.62e-03 1e+00 abnormal pons morphology 7.47e-03 1e+00 sinus inflammation 7.47e-03 1e+00 dilated uterine cervix 9.33e-03 1e+00 increased placenta weight 9.33e-03 1e+00 neuronal cytoplasmic inclusions 9.33e-03 1e+00 abnormal pancreatic beta cell differentiation 9.34e-03 1e+00 poor grooming 1.12e-02 1e+00 hyperpigmentation 1.12e-02 1e+00 ectopic cerebellar granule cells

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

²FDR corrected p-value (Benjamini-Hochberg)