Back to main page

DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod75

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod75 Module size 85 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 135927 C7orf34 LLLL and CFNLAS motif containing 1 9486 CHST10 carbohydrate sulfotransferase 10 1452 CSNK1A1 casein kinase 1 alpha 1 122011 CSNK1A1L casein kinase 1 alpha 1 like 1472 CST4 cystatin S 81558 FAM117A family with sequence similarity 117 member A 64839 FBXL17 F-box and leucine rich repeat protein 17 26235 FBXL4 F-box and leucine rich repeat protein 4 26233 FBXL6 F-box and leucine rich repeat protein 6 84922 FIZ1 FLT3 interacting zinc finger 1 3169 FOXA1 forkhead box A1 3170 FOXA2 forkhead box A2 3171 FOXA3 forkhead box A3 27023 FOXB1 forkhead box B1 442425 FOXB2 forkhead box B2 2290 FOXG1 forkhead box G1 8928 FOXH1 forkhead box H1 221937 FOXK1 forkhead box K1 3607 FOXK2 forkhead box K2 2305 FOXM1 forkhead box M1 2308 FOXO1 forkhead box O1 2309 FOXO3 forkhead box O3 4303 FOXO4 forkhead box O4 100132074 FOXO6 forkhead box O6 93986 FOXP2 forkhead box P2 2580 GAK cyclin G associated kinase 499214 GCK cytochrome c oxidase assembly factor 4 homolog 55668 GPATCH2L G-patch domain containing 2 like 8925 HERC1 HECT and RLD domain containing E3 ubiquitin protein ligase family member 1 8924 HERC2 HECT and RLD domain containing E3 ubiquitin protein ligase 2 3096 HIVEP1 human immunodeficiency virus type I enhancer binding protein 1 10527 IPO7 importin 7 10526 IPO8 importin 8 80853 JHDM1D lysine demethylase 7A 55693 KDM4D lysine demethylase 4D 390245 KDM4E lysine demethylase 4E 26231 LRRC29 leucine rich repeat containing 29 4207 MEF2B BORCS8-MEF2B readthrough 4814 NINJ1 ninjurin 1 57523 NYNRIN NYN domain and retroviral integrase containing 5253 PHF2 PHD finger protein 2 23133 PHF8 PHD finger protein 8 91461 PKDCC protein kinase domain containing, cytoplasmic 5530 PPP3CA protein phosphatase 3 catalytic subunit alpha 63977 PRDM15 PR/SET domain 15 80758 PRR7 proline rich 7, synaptic 25788 RAD54B RAD54 homolog B 162494 RHBDL3 rhomboid like 3 6648 SOD2 superoxide dismutase 2 57057 TBX20 T-box 20 7030 TFE3 transcription factor binding to IGHM enhancer 3 7942 TFEB transcription factor EB 84630 TTBK1 tau tubulin kinase 1 146057 TTBK2 tau tubulin kinase 2 9686 VGLL4 vestigial like family member 4 7443 VRK1 VRK serine/threonine kinase 1 51231 VRK3 VRK serine/threonine kinase 3 57510 XPO5 exportin 5 23214 XPO6 exportin 6 22803 XRN2 5'-3' exoribonuclease 2 22890 ZBTB1 zinc finger and BTB domain containing 1 27107 ZBTB11 zinc finger and BTB domain containing 11 7597 ZBTB25 zinc finger and BTB domain containing 25 3104 ZBTB48 zinc finger and BTB domain containing 48 643836 ZFP62 ZFP62 zinc finger protein 23660 ZKSCAN5 zinc finger with KRAB and SCAN domains 5 7697 ZNF138 zinc finger protein 138 10472 ZNF238 zinc finger and BTB domain containing 18 58500 ZNF250 zinc finger protein 250 339324 ZNF260 zinc finger protein 260 9422 ZNF264 zinc finger protein 264 92822 ZNF276 zinc finger protein 276 55422 ZNF331 zinc finger protein 331 55628 ZNF407 zinc finger protein 407 161882 ZNF408 zinc finger protein, FOG family member 1 7596 ZNF45 zinc finger protein 45 25888 ZNF473 zinc finger protein 473 137209 ZNF572 zinc finger protein 572 440077 ZNF705A zinc finger protein 705A 100132396 ZNF705B zinc finger protein 705B 728957 ZNF705D zinc finger protein 705D 100131980 ZNF705G zinc finger protein 705G 100289678 ZNF783 zinc finger family member 783 146540 ZNF785 zinc finger protein 785 284312 ZSCAN1 zinc finger and SCAN domain containing 1

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 1.34e-01 5.12e-06 Reactome AKT phosphorylates targets in the nucleus Signal Transduction 1.10e-01 2.32e-07 GO histone demethylase activity (H3-K9 specific) molecular_function 9.05e-02 8.02e-03 Reactome Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) Disease 4.93e-02 2.19e-05 GO cellular glucose homeostasis biological_process 3.38e-02 1.00e-05 GO histone demethylase activity (H3-K36 specific) molecular_function 2.33e-02 1.01e-05 GO Ran GTPase binding molecular_function 2.23e-02 1.91e-07 GO peptidyl-threonine phosphorylation biological_process 1.37e-02 2.19e-05 Reactome Regulation of gene expression in beta cells Developmental Biology 1.32e-02 1.95e-05 GO SCF-dependent proteasomal ubiquitin-dependent protein catabolic process biological_process 9.49e-03 3.15e-07 GO histone H3-K9 demethylation biological_process 5.35e-03 1.21e-03 GO cardiac right ventricle morphogenesis 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 6.75e-10 3.67e-07 RNA polymerase II transcription factor activity, sequence-specific DNA binding 6.64e-06 2.67e-03 histone H3-K9 demethylation 1.82e-05 4.52e-03 histone demethylase activity (H3-K9 specific) 2.25e-05 5.49e-03 Ran GTPase binding 4.28e-05 1.40e-02 transcription from RNA polymerase II promoter 4.46e-05 1.45e-02 regulation of chromatin silencing at rDNA 5.05e-05 1.62e-02 regulation of cell shape 5.56e-05 1.76e-02 cellular glucose homeostasis 9.19e-05 1.92e-02 transcription regulatory region DNA binding 9.40e-05 1.96e-02 regulatory region DNA binding 9.75e-05 2.86e-02 peptidyl-serine phosphorylation 1.02e-04 2.97e-02 response to water-immersion restraint stress 1.14e-04 3.27e-02 histone lysine demethylation 1.16e-04 3.32e-02 regulation of gene silencing 1.40e-04 3.88e-02 glucose homeostasis 1.40e-04 3.88e-02 carbohydrate homeostasis 1.46e-04 4.03e-02 histone demethylation 2.21e-04 5.70e-02 protein demethylation 2.38e-04 6.07e-02 muscle organ development 2.87e-04 5.19e-02 histone demethylase activity

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 3.47e-07 8.34e-05 REGULATION OF GENE EXPRESSION IN BETA CELLS 1.26e-06 2.15e-04 REGULATION OF GENE EXPRESSION IN BETA CELLS 1.64e-06 3.56e-04 REGULATION OF BETA CELL DEVELOPMENT 3.28e-06 5.28e-04 REGULATION OF BETA CELL DEVELOPMENT 3.38e-04 3.82e-02 PIP3 ACTIVATES AKT SIGNALING 4.30e-04 4.74e-02 PI3K EVENTS IN ERBB4 SIGNALING 6.23e-04 6.58e-02 PI3K AKT ACTIVATION 6.32e-04 6.67e-02 PI3K EVENTS IN ERBB2 SIGNALING 6.78e-04 7.11e-02 GAB1 SIGNALOSOME 7.57e-04 9.21e-02 PIP3 ACTIVATES AKT SIGNALING 8.32e-04 1.00e-01 GENERIC TRANSCRIPTION PATHWAY 1.11e-03 1.11e-01 SIGNALING BY NODAL 1.16e-03 1.34e-01 PI3K EVENTS IN ERBB4 SIGNALING 1.42e-03 1.59e-01 DEVELOPMENTAL BIOLOGY 1.63e-03 1.79e-01 GAB1 SIGNALOSOME 1.72e-03 1.87e-01 SIGNALING BY NODAL 1.77e-03 1.91e-01 PI3K AKT ACTIVATION 1.79e-03 1.93e-01 PI3K EVENTS IN ERBB2 SIGNALING 2.59e-03 2.34e-01 PI 3K CASCADE 4.71e-03 3.91e-01 SIGNALING BY SCF KIT

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 1.76e-03 1e+00 increased cellular sensitivity to gamma-irradiation 1.93e-03 1e+00 fused somites 2.53e-03 1e+00 embryonic-extraembryonic boundary constriction 3.63e-03 1e+00 absent notochord 4.53e-03 1e+00 absent primitive node 6.36e-03 1e+00 abnormal circulating insulin level 8.45e-03 1e+00 decreased somite size 9.36e-03 1e+00 abnormal somite shape 1.01e-02 1e+00 disorganized myocardium 1.10e-02 1e+00 abnormal spermatid morphology 1.28e-02 1e+00 decreased glycogen level 1.30e-02 1e+00 increased circulating ketone body level 1.31e-02 1e+00 increased prolactinoma incidence 1.31e-02 1e+00 galactostasis 1.36e-02 1e+00 enlarged myocardial fiber 1.41e-02 1e+00 abnormal glucose homeostasis 1.53e-02 1e+00 failure of heart looping 1.55e-02 1e+00 holoprosencephaly 1.55e-02 1e+00 abnormal thalamus morphology 1.68e-02 1e+00 abnormal cellular replicative senescence

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

²FDR corrected p-value (Benjamini-Hochberg)