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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod352

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod352 Module size 75 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 4185 ADAM11 ADAM metallopeptidase domain 11 11086 ADAM29 ADAM metallopeptidase domain 29 23300 ATMIN ATM interactor 64979 BRIP1 mitochondrial ribosomal protein L36 9024 BRSK2 BR serine/threonine kinase 2 84419 C15orf48 chromosome 15 open reading frame 48 112770 C1orf85 glycosylated lysosomal membrane protein 823 CAPN1 calpain 1 1406 CRX cone-rod homeobox 79004 CUEDC2 CUE domain containing 2 285489 DOK7 docking protein 7 10589 DRAP1 DR1 associated protein 1 1958 EGR1 early growth response 1 10919 EHMT2 euchromatic histone lysine methyltransferase 2 90187 EMILIN3 elastin microfibril interfacer 3 55914 ERBB2IP erbb2 interacting protein 57471 ERMN ermin 56975 FAM20C FAM20C, golgi associated secretory pathway kinase 287570 GAS2 growth arrest-specific 2 like 2 8521 GCM1 glial cells missing homolog 1 2957 GTF2A1 general transcription factor IIA subunit 1 51191 HERC5 HECT and RLD domain containing E3 ubiquitin protein ligase 5 359948 IRF2BP2 interferon regulatory factor 2 binding protein 2 25959 KANK2 KN motif and ankyrin repeat domains 2 9772 KIAA0195 transmembrane protein 94 283638 KIAA0284 centrosomal protein 170B 205717 KIAA2018 upstream transcription factor family member 3 146909 KIF18B kinesin family member 18B 23276 KLHL18 kelch like family member 18 84626 KRBA1 KRAB-A domain containing 1 3882 KRT32 keratin 32 337880 KRTAP11-1 keratin associated protein 11-1 84232 MAF1 MAF1 homolog, negative regulator of RNA polymerase III 149175 MANEAL mannosidase endo-alpha like 8888 MCM3AP minichromosome maintenance complex component 3 associated protein 4204 MECP2 methyl-CpG binding protein 2 60672 MIIP migration and invasion inhibitory protein 4338 MOCS2 molybdenum cofactor synthesis 2 55154 MSTO1 misato 1, mitochondrial distribution and morphology regulator 4861 NPAS1 neuronal PAS domain protein 1 221443 OARD1 O-acyl-ADP-ribose deacylase 1 54681 P4HTM prolyl 4-hydroxylase, transmembrane 23239 PHLPP1 PH domain and leucine rich repeat protein phosphatase 1 23035 PHLPP2 PH domain and leucine rich repeat protein phosphatase 2 5266 PI3 peptidase inhibitor 3 5494 PPM1A protein phosphatase, Mg2+/Mn2+ dependent 1A 51422 PRKAG2 protein kinase AMP-activated non-catalytic subunit gamma 2 5673 PSG5 pregnancy specific beta-1-glycoprotein 5 171558 PTCRA pre T cell antigen receptor alpha 375287 RBM43 RNA binding motif protein 43 401190 RGS7BP regulator of G protein signaling 7 binding protein 8737 RIPK1 receptor interacting serine/threonine kinase 1 8767 RIPK2 receptor interacting serine/threonine kinase 2 11035 RIPK3 receptor interacting serine/threonine kinase 3 23248 RPRD2 regulation of nuclear pre-mRNA domain containing 2 29901 SAC3D1 SAC3 domain containing 1 163786 SASS6 SAS-6 centriolar assembly protein 6492 SIM1 SIM bHLH transcription factor 1 80704 SLC19A3 solute carrier family 19 member 3 6663 SOX10 SRY-box 10 6666 SOX12 SRY-box 12 80320 SP6 Sp6 transcription factor 6722 SRF serum response factor 286749 STON1-GTF2A1L STON1-GTF2A1L readthrough 8148 TAF15 TATA-box binding protein associated factor 15 54790 TET2 tet methylcytosine dioxygenase 2 54881 TEX10 testis expressed 10 7153 TOP2A DNA topoisomerase II alpha 7155 TOP2B DNA topoisomerase II beta 57761 TRIB3 tribbles pseudokinase 3 8295 TRRAP transformation/transcription domain associated protein 10782 ZNF274 zinc finger protein 274 10794 ZNF460 zinc finger protein 460 221785 ZNF498 zinc finger and SCAN domain containing 25 121274 ZNF641 zinc finger protein 641

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 1.10e-01 2.03e-04 GO transcription factor TFIIA complex cellular_component 1.03e-01 2.03e-04 Reactome TLR3-mediated TICAM1-dependent programmed cell death Immune System 4.63e-02 3.77e-04 GO JUN kinase kinase kinase activity molecular_function 1.98e-02 7.36e-04 GO DNA topological change biological_process 5.33e-03 1.04e-03 GO startle response 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 1.02e-04 2.11e-02 DNA topoisomerase type II (ATP-hydrolyzing) activity 2.76e-04 4.80e-02 ripoptosome 3.49e-04 6.15e-02 double-stranded methylated DNA binding 3.79e-04 6.60e-02 DNA topoisomerase activity 5.13e-04 1.14e-01 positive regulation of necrotic cell death 6.36e-04 1.36e-01 amyloid fibril formation 6.37e-04 1.04e-01 histone deacetylase binding 6.63e-04 1.41e-01 reciprocal meiotic recombination 8.16e-04 1.67e-01 peptidyl-lysine modification 1.13e-03 2.18e-01 regulation of histone H3-K9 trimethylation 1.27e-03 2.40e-01 DNA topological change 1.52e-03 2.78e-01 resolution of meiotic recombination intermediates 1.52e-03 2.22e-01 chromatin binding 1.70e-03 3.04e-01 meiotic chromosome segregation 1.95e-03 3.34e-01 meiotic chromosome separation 2.07e-03 2.90e-01 RNA polymerase II transcription factor activity, sequence-specific DNA binding 2.42e-03 3.33e-01 transcription factor activity, transcription factor binding 2.58e-03 3.51e-01 transcription factor activity, protein binding 2.85e-03 4.54e-01 histone methylation 2.90e-03 4.60e-01 keratinization

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 9.39e-04 1.12e-01 NEGATIVE REGULATION OF THE PI3K AKT NETWORK 1.00e-03 1.00e-01 NEGATIVE REGULATION OF THE PI3K AKT NETWORK 2.15e-03 2.27e-01 REGULATION OF AMPK ACTIVITY VIA LKB1 2.40e-03 2.18e-01 REGULATION OF AMPK ACTIVITY VIA LKB1 3.21e-03 3.19e-01 ENERGY DEPENDENT REGULATION OF MTOR BY LKB1 AMPK 3.42e-03 2.97e-01 ENERGY DEPENDENT REGULATION OF MTOR BY LKB1 AMPK 5.16e-03 4.69e-01 RIP MEDIATED NFKB ACTIVATION VIA DAI 5.66e-03 4.54e-01 RIP MEDIATED NFKB ACTIVATION VIA DAI 7.59e-03 5.85e-01 PI3K CASCADE 7.88e-03 6.63e-01 PI3K CASCADE 9.95e-03 7.30e-01 PKB MEDIATED EVENTS 1.04e-02 8.21e-01 PKB MEDIATED EVENTS 1.15e-02 8.23e-01 TRIF MEDIATED TLR3 SIGNALING 1.16e-02 8.96e-01 TRIF MEDIATED TLR3 SIGNALING 1.37e-02 9.46e-01 METABOLISM OF VITAMINS AND COFACTORS 1.40e-02 9.61e-01 INSULIN RECEPTOR SIGNALLING CASCADE 1.44e-02 1.00e+00 PIP3 ACTIVATES AKT SIGNALING 1.45e-02 1.00e+00 INSULIN RECEPTOR SIGNALLING CASCADE 1.46e-02 1.00e+00 METABOLISM OF VITAMINS AND COFACTORS 1.52e-02 1.00e+00 PIP3 ACTIVATES AKT SIGNALING

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 3.18e-04 4.67e-01 abnormal body temperature 3.23e-04 4.71e-01 absent enamel 3.90e-04 5.24e-01 abnormal tooth hard tissue morphology 6.40e-04 6.98e-01 delayed circadian phase 3.33e-03 1.00e+00 abnormal tooth morphology 3.65e-03 1.00e+00 akinesia 4.12e-03 1.00e+00 Leydig cell hypoplasia 4.31e-03 1.00e+00 absent vibrissae 5.42e-03 1.00e+00 abnormal dentin morphology 5.66e-03 1.00e+00 sporadic seizures 7.25e-03 1.00e+00 abnormal leukocyte cell number 7.84e-03 1.00e+00 abnormal long term object recognition memory 8.23e-03 1.00e+00 abnormal innervation pattern to muscle 9.15e-03 1.00e+00 abnormal jaw morphology 1.08e-02 1.00e+00 neonatal lethality 1.11e-02 1.00e+00 abnormal brown adipose tissue morphology 1.12e-02 1.00e+00 decreased circulating phospholipid level 1.12e-02 1.00e+00 supernumerary incisors 1.24e-02 1.00e+00 decreased neuron number 1.31e-02 1.00e+00 dorsal root ganglion hypoplasia

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

²FDR corrected p-value (Benjamini-Hochberg)