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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod328

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod328 Module size 55 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 51225 ABI3 ABI family member 3 2334 AFF2 AF4/FMR2 family member 2 3899 AFF3 AF4/FMR2 family member 3 124930 ANKRD13B ankyrin repeat domain 13B 338692 ANKRD13D ankyrin repeat domain 13D 57020 C16orf62 VPS35 endosomal protein sorting factor like 54785 C17orf59 BLOC-1 related complex subunit 6 151195 CCNYL1 cyclin Y like 1 414194 CCNYL2 cyclin Y-like 2 (pseudogene) 138009 DCAF4L2 DDB1 and CUL4 associated factor 4 like 2 149095 DCST1 DC-STAMP domain containing 1 127579 DCST2 DC-STAMP domain containing 2 80821 DDHD1 DDHD domain containing 1 27351 DESI1 desumoylating isopeptidase 1 51029 DESI2 desumoylating isopeptidase 2 9829 DNAJC6 DnaJ heat shock protein family (Hsp40) member C6 57579 FAM135A family with sequence similarity 135 member A 80011 FAM192A family with sequence similarity 192 member A 84895 FAM73B mitoguardin 2 200933 FBXO45 F-box protein 45 84261 FBXW9 F-box and WD repeat domain containing 9 266977 GPR110 adhesion G protein-coupled receptor F1 11104 KATNA1 katanin catalytic subunit A1 84056 KATNAL1 katanin catalytic subunit A1 like 1 83473 KATNAL2 katanin catalytic subunit A1 like 2 114294 LACTB lactamase beta 255231 MCOLN2 mucolipin 2 55283 MCOLN3 mucolipin 3 23077 MYCBP2 MYC binding protein 2, E3 ubiquitin protein ligase 28512 NKIRAS1 NFKB inhibitor interacting Ras like 1 28511 NKIRAS2 NFKB inhibitor interacting Ras like 2 8131 NPRL3 NPR3 like, GATOR1 complex subunit 197135 PATL2 PAT1 homolog 2 5238 PGM3 phosphoglucomutase 3 150379 PNPLA5 patatin like phospholipase domain containing 5 146547 PRSS36 serine protease 36 339105 PRSS53 serine protease 53 5728 PTEN phosphatase and tensin homolog 26750 RPS6KC1 ribosomal protein S6 kinase C1 83694 RPS6KL1 ribosomal protein S6 kinase like 1 29907 SNX15 sorting nexin 15 84888 SPPL2A signal peptide peptidase like 2A 162540 SPPL2C signal peptide peptidase like 2C 295344 ST7 suppression of tumorigenicity 7-like 54879 ST7L suppression of tumorigenicity 7 like 6954 TCP11 t-complex 11 55346 TCP11L1 t-complex 11 like 1 255394 TCP11L2 t-complex 11 like 2 23371 TENC1 tensin 2 360200 TMPRSS9 transmembrane serine protease 9 7145 TNS1 tensin 1 64759 TNS3 tensin 3 7179 TPTE transmembrane phosphatase with tensin homology 93492 TPTE2 transmembrane phosphoinositide 3-phosphatase and tensin homolog 2 65267 WNK3 WNK lysine deficient protein kinase 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 1.98e-01 4.39e-07 GO microtubule severing biological_process 9.70e-02 8.29e-05 GO integral component of cytoplasmic side of endoplasmic reticulum membrane cellular_component 2.17e-02 2.06e-06 GO microtubule-severing ATPase activity molecular_function 1.60e-02 1.16e-04 GO aspartic endopeptidase activity, intramembrane cleaving molecular_function 6.52e-03 4.26e-04 GO cardiac muscle tissue development biological_process

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 3.73e-06 1.06e-03 microtubule-severing ATPase activity 4.93e-06 1.37e-03 phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity 6.16e-06 1.68e-03 phosphatidylinositol trisphosphate phosphatase activity 3.23e-05 7.15e-03 integral component of cytoplasmic side of endoplasmic reticulum membrane 5.21e-05 1.66e-02 cytoplasmic microtubule organization 5.35e-05 1.70e-02 peptidyl-tyrosine dephosphorylation 1.05e-04 2.04e-02 cytoplasmic side of endoplasmic reticulum membrane 1.80e-04 3.45e-02 protein tyrosine phosphatase activity 2.24e-04 5.76e-02 regulation of cyclin-dependent protein serine/threonine kinase activity 2.56e-04 6.45e-02 microtubule severing 2.62e-04 6.58e-02 central nervous system neuron axonogenesis 2.96e-04 5.34e-02 protein tyrosine/serine/threonine phosphatase activity 7.56e-04 1.57e-01 membrane protein intracellular domain proteolysis 8.54e-04 1.74e-01 protein dephosphorylation 9.13e-04 1.83e-01 membrane protein ectodomain proteolysis 9.58e-04 1.41e-01 integral component of lumenal side of endoplasmic reticulum membrane 1.10e-03 1.67e-01 phosphatidylinositol bisphosphate phosphatase activity 1.38e-03 2.04e-01 aspartic-type endopeptidase activity 1.43e-03 2.10e-01 phosphoprotein phosphatase activity 1.60e-03 2.32e-01 aspartic-type peptidase activity

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 6.03e-04 6.40e-02 PI METABOLISM 1.18e-03 1.36e-01 PI METABOLISM 7.41e-03 5.73e-01 PHOSPHOLIPID METABOLISM 9.30e-03 7.56e-01 PHOSPHOLIPID METABOLISM 1.00e-02 7.32e-01 SYNTHESIS OF PIPS AT THE GOLGI MEMBRANE 1.20e-02 9.20e-01 NEGATIVE REGULATION OF THE PI3K AKT NETWORK 1.26e-02 8.86e-01 NEGATIVE REGULATION OF THE PI3K AKT NETWORK 1.31e-02 9.85e-01 SYNTHESIS OF SUBSTRATES IN N GLYCAN BIOSYTHESIS 1.64e-02 1.00e+00 BIOSYNTHESIS OF THE N GLYCAN PRECURSOR DOLICHOL LIPID LINKED OLIGOSACCHARIDE LLO AND TRANSFER TO A NASCENT PROTEIN 1.69e-02 1.00e+00 SYNTHESIS OF PIPS AT THE GOLGI MEMBRANE 2.49e-02 1.00e+00 LYSOSOME VESICLE BIOGENESIS 2.88e-02 1.00e+00 SYNTHESIS OF PIPS AT THE PLASMA MEMBRANE 3.08e-02 1.00e+00 LYSOSOME VESICLE BIOGENESIS 3.48e-02 1.00e+00 SYNTHESIS OF SUBSTRATES IN N GLYCAN BIOSYTHESIS 3.52e-02 1.00e+00 SYNTHESIS OF PIPS AT THE PLASMA MEMBRANE 4.53e-02 1.00e+00 PIP3 ACTIVATES AKT SIGNALING 4.58e-02 1.00e+00 GOLGI ASSOCIATED VESICLE BIOGENESIS 4.61e-02 1.00e+00 BIOSYNTHESIS OF THE N GLYCAN PRECURSOR DOLICHOL LIPID LINKED OLIGOSACCHARIDE LLO AND TRANSFER TO A NASCENT PROTEIN 4.76e-02 1.00e+00 PIP3 ACTIVATES AKT SIGNALING 4.77e-02 1.00e+00 DOWNSTREAM TCR SIGNALING

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 1.34e-03 1e+00 absent anterior commissure 3.74e-03 1e+00 jumpy 3.77e-03 1e+00 increased endometrial carcinoma incidence 5.63e-03 1e+00 increased prostate gland tumor incidence 5.64e-03 1e+00 increased hamartoma incidence 7.48e-03 1e+00 absent sperm mitochondrial sheath 7.49e-03 1e+00 decreased renal plasma flow rate 7.52e-03 1e+00 increased thyroid adenoma incidence 9.35e-03 1e+00 abnormal spinal cord grey matter morphology 9.37e-03 1e+00 increased thyroid carcinoma incidence 9.38e-03 1e+00 variegated coat color 9.51e-03 1e+00 decreased circulating serum albumin level 1.05e-02 1e+00 abnormal motor neuron morphology 1.12e-02 1e+00 detached tectorial membrane 1.12e-02 1e+00 increased prostate intraepithelial neoplasia incidence 1.12e-02 1e+00 increased teratoma incidence 1.12e-02 1e+00 abnormal thyroid follicular cell morphology 1.12e-02 1e+00 decreased activation-induced B cell apoptosis 1.31e-02 1e+00 increased thyroid tumor incidence 1.31e-02 1e+00 increased adrenal gland tumor incidence

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

²FDR corrected p-value (Benjamini-Hochberg)