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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod358

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod358 Module size 45 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 83543 AIF1L allograft inflammatory factor 1 like 79647 AKIRIN1 akirin 1 91369 ANKRD40 ankyrin repeat domain 40 10904 BLCAP BLCAP, apoptosis inducing factor 339448 C1orf174 chromosome 1 open reading frame 174 113444 C1orf212 small integral membrane protein 12 25966 C2CD2 C2 calcium dependent domain containing 2 56892 C8orf4 transcriptional and immune response regulator 203197 C9orf91 transmembrane protein 268 23271 CAMSAP2 calmodulin regulated spectrin associated protein family member 2 8545 CGGBP1 CGG triplet repeat binding protein 1 9811 CTIF cap binding complex dependent translation initiation factor 23258 DENND5A DENN domain containing 5A 23167 EFR3A EFR3 homolog A 54566 EPB41L4B erythrocyte membrane protein band 4.1 like 4B 90362 FAM110B family with sequence similarity 110 member B 10827 FAM114A2 family with sequence similarity 114 member A2 54065 FAM165B small integral membrane protein 11A 83989 FAM172A family with sequence similarity 172 member A 157638 FAM84B family with sequence similarity 84 member B 84256 FLYWCH1 FLYWCH-type zinc finger 1 64778 FNDC3B fibronectin type III domain containing 3B 83786 FRMD8 FERM domain containing 8 27333 GOLIM4 golgi integral membrane protein 4 60313 GPBP1L1 GC-rich promoter binding protein 1 like 1 64224 HERPUD2 HERPUD family member 2 9665 KIAA0430 meiosis regulator and mRNA stability factor 1 51315 KRCC1 lysine rich coiled-coil 1 63905 MANBAL mannosidase beta like 54542 RC3H2 ring finger and CCCH-type domains 2 83695 RHNO1 RAD9-HUS1-RAD1 interacting nuclear orphan 1 9673 SLC25A44 solute carrier family 25 member 44 254428 SLC41A1 solute carrier family 41 member 1 93643 TJAP1 tight junction associated protein 1 4071 TM4SF1 transmembrane 4 L six family member 1 148534 TMEM56 transmembrane protein 56 84899 TMTC4 transmembrane and tetratricopeptide repeat containing 4 27075 TSPAN13 tetraspanin 13 6302 TSPAN31 tetraspanin 31 23548 TTC33 tetratricopeptide repeat domain 33 7288 TULP2 tubby like protein 2 5412 UBL3 ubiquitin like 3 154807 VKORC1L1 vitamin K epoxide reductase complex subunit 1 like 1 286046 XKR6 XK related 6 85364 ZCCHC3 zinc finger CCHC-type containing 3

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 2.79e-02 3.32e-03 Reactome Metabolism of vitamin K Metabolism

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 1.95e-03 3.34e-01 T follicular helper cell differentiation 2.48e-03 3.40e-01 microtubule minus-end binding 2.85e-03 3.54e-01 bicellular tight junction 3.01e-03 3.69e-01 apical junction complex 3.89e-03 5.71e-01 protein localization to photoreceptor outer segment 3.90e-03 5.71e-01 positive regulation of NF-kappaB import into nucleus 3.90e-03 5.71e-01 positive regulation of keratinocyte migration 5.40e-03 6.53e-01 divalent inorganic cation transmembrane transporter activity 5.84e-03 7.72e-01 cellular response to magnesium ion 5.84e-03 7.72e-01 endothelial cell activation 5.84e-03 7.72e-01 B cell homeostasis 5.84e-03 7.72e-01 positive regulation of G0 to G1 transition 7.77e-03 9.47e-01 receptor localization to non-motile cilium 7.77e-03 9.47e-01 protein localization to ciliary membrane 7.77e-03 9.47e-01 vitamin K metabolic process 7.78e-03 9.47e-01 response to magnesium ion 7.78e-03 9.47e-01 T-helper cell differentiation 7.78e-03 9.47e-01 peptidyl-glutamic acid carboxylation 7.79e-03 9.47e-01 T cell differentiation involved in immune response 7.80e-03 9.47e-01 positive regulation of transcription factor import into nucleus

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 3.63e-03 3.5e-01 METAL ION SLC TRANSPORTERS 3.80e-02 1.0e+00 TRANSPORT OF GLUCOSE AND OTHER SUGARS BILE SALTS AND ORGANIC ACIDS METAL IONS AND AMINE COMPOUNDS

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 increased macrophage cytokine production 1.89e-03 1e+00 abnormal lung development 3.74e-03 1e+00 abnormal lung alveolus development 3.78e-03 1e+00 increased tumor necrosis factor secretion 3.80e-03 1e+00 abnormal female meiosis I arrest 5.72e-03 1e+00 abnormal bone ossification 7.18e-03 1e+00 decreased fibroblast cell migration 7.53e-03 1e+00 abnormal cell differentiation 1.13e-02 1e+00 abnormal cell adhesion 1.50e-02 1e+00 decreased fibroblast proliferation 2.78e-02 1e+00 decreased circulating insulin level 3.89e-02 1e+00 female infertility

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

²FDR corrected p-value (Benjamini-Hochberg)