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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod259

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod259 Module size 31 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 84890 ADO 2-aminoethanethiol dioxygenase 120534 ARL14EP ADP ribosylation factor like GTPase 14 effector protein 644100 ARL14EPL ADP ribosylation factor like GTPase 14 effector protein like 605 BCL7A BCL tumor suppressor 7A 9275 BCL7B BCL tumor suppressor 7B 65980 BRD9 bromodomain containing 9 124817 CNTD1 cyclin N-terminal domain containing 1 64506 CPEB1 cytoplasmic polyadenylation element binding protein 1 1497 CTNS cystinosin, lysosomal cystine transporter 85406 DNAJC14 DnaJ heat shock protein family (Hsp40) member C14 135656 DPCR1 mucin like 3 159090 FAM122B family with sequence similarity 122B 8733 GPAA1 glycosylphosphatidylinositol anchor attachment 1 91133 L3MBTL4 L3MBTL4, histone methyl-lysine binding protein 92255 LMBRD2 LMBR1 domain containing 2 26002 MOXD1 monooxygenase DBH like 1 9633 MTL5 testis expressed metallothionein like protein 28962 OSTM1 osteoclastogenesis associated transmembrane protein 1 64773 PCED1A PC-esterase domain containing 1A 91523 PCED1B PC-esterase domain containing 1B 55650 PIGV phosphatidylinositol glycan anchor biosynthesis class V 5511 PPP1R8 protein phosphatase 1 regulatory subunit 8 4810 SCML1 NHS actin remodeling regulator 256380 SCML4 Scm polycomb group protein like 4 83932 SPRTN SprT-like N-terminal domain 51188 SS18L2 SS18 like 2 84928 TMEM209 transmembrane protein 209 55706 TMEM48 NDC1 transmembrane nucleoporin 26262 TSPAN17 tetraspanin 17 10098 TSPAN5 tetraspanin 5 57599 WDR48 WD repeat domain 48

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 2.47e-04 6.25e-02 GPI anchor metabolic process 2.47e-04 6.25e-02 GPI anchor biosynthetic process 6.22e-04 1.34e-01 glycolipid biosynthetic process 1.02e-03 1.56e-01 L-cystine transmembrane transporter activity 1.65e-03 2.96e-01 phenol-containing compound metabolic process 1.95e-03 3.34e-01 regulation of protein monoubiquitination 1.95e-03 3.34e-01 norepinephrine biosynthetic process 3.90e-03 5.71e-01 negative regulation of cytoplasmic translation 4.42e-03 5.02e-01 mannosyltransferase complex 4.70e-03 6.62e-01 glycolipid metabolic process 5.21e-03 6.33e-01 GPI anchor binding 5.28e-03 5.81e-01 GPI-anchor transamidase complex 5.31e-03 5.83e-01 messenger ribonucleoprotein complex 5.68e-03 6.82e-01 GPI-anchor transamidase activity 5.84e-03 7.72e-01 preassembly of GPI anchor in ER membrane 5.84e-03 7.72e-01 norepinephrine metabolic process 5.84e-03 7.72e-01 dopamine catabolic process 5.84e-03 7.72e-01 protein retention in ER lumen 5.84e-03 7.72e-01 maintenance of protein localization in endoplasmic reticulum 5.84e-03 7.72e-01 melanin biosynthetic process

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 8.62e-05 1.11e-02 POST TRANSLATIONAL MODIFICATION SYNTHESIS OF GPI ANCHORED PROTEINS 7.14e-04 8.74e-02 POST TRANSLATIONAL MODIFICATION SYNTHESIS OF GPI ANCHORED PROTEINS 1.83e-03 1.72e-01 POST TRANSLATIONAL PROTEIN MODIFICATION 1.11e-02 8.65e-01 POST TRANSLATIONAL PROTEIN MODIFICATION 1.25e-02 8.83e-01 SYNTHESIS OF GLYCOSYLPHOSPHATIDYLINOSITOL GPI 3.56e-02 1.00e+00 SYNTHESIS OF GLYCOSYLPHOSPHATIDYLINOSITOL GPI

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 failure of secondary bone resorption 1.87e-03 1e+00 corneal deposits 3.74e-03 1e+00 dilated mitochondria 3.75e-03 1e+00 abnormal molar crown morphology 3.75e-03 1e+00 failure of tooth eruption 5.61e-03 1e+00 failure of bone ossification 5.61e-03 1e+00 abnormal deltoid tuberosity morphology 7.48e-03 1e+00 short incisors 9.32e-03 1e+00 small proamniotic cavity 9.32e-03 1e+00 abnormal ovary development 9.33e-03 1e+00 abnormal proamniotic cavity morphology 9.83e-03 1e+00 reduced male fertility 1.09e-02 1e+00 decreased bone mineral density 1.12e-02 1e+00 double outlet right ventricle with atrioventricular septal defect 1.12e-02 1e+00 absent incisors 1.12e-02 1e+00 osteopetrosis 1.12e-02 1e+00 partial lethality at weaning 1.12e-02 1e+00 abnormal maxilla morphology 1.12e-02 1e+00 absent ovary 1.30e-02 1e+00 abnormal extraembryonic ectoderm morphology

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

²FDR corrected p-value (Benjamini-Hochberg)