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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod281

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod281 Module size 78 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 305577 AHSA1 activator of HSP90 ATPase homolog 2 130872 AHSA2 activator of HSP90 ATPase homolog 2, pseudogene 57379 AICDA activation induced cytidine deaminase 9049 AIP aryl hydrocarbon receptor interacting protein 23746 AIPL1 aryl hydrocarbon receptor interacting protein like 1 8846 ALKBH1 alkB homolog 1, histone H2A dioxygenase 80216 ALPK1 alpha kinase 1 573 BAG1 BCL2 associated athanogene 1 9532 BAG2 BCL2 associated athanogene 2 114897 C1QTNF1 C1q and TNF related 1 114904 C1QTNF6 C1q and TNF related 6 25943 C20orf194 chromosome 20 open reading frame 194 85438 CABS1 calcium binding protein, spermatid associated 1 27101 CACYBP calcyclin binding protein 79823 CAMKMT calmodulin-lysine N-methyltransferase 150275 CCDC117 coiled-coil domain containing 117 11140 CDC37 cell division cycle 37 55664 CDC37L1 cell division cycle 37 like 1 26973 CHORDC1 cysteine and histidine rich domain containing 1 23529 CLC cardiotrophin like cytokine factor 1 81035 COLEC12 collectin subfamily member 12 83690 CRISPLD1 cysteine rich secretory protein LCCL domain containing 1 1413 CRYBA4 crystallin beta A4 162989 DEDD2 death effector domain containing 2 63951 DMRTA1 DMRT like family A1 8721 EDF1 endothelial differentiation related factor 1 55194 EVA1B eva-1 homolog B 144699 FBXL14 F-box and leucine rich repeat protein 14 26261 FBXO24 F-box protein 24 51725 FBXO40 F-box protein 40 2765 GML glycosylphosphatidylinositol anchored molecule like 100192205 HSBP1 heat shock factor binding protein 1-like 1 3320 HSP90AA1 heat shock protein 90 alpha family class A member 1 3326 HSP90AB1 heat shock protein 90 alpha family class B member 1 3312 HSPA8 heat shock protein family A (Hsp70) member 8 79713 IGFLR1 IGF like family receptor 1 386617 KCTD8 potassium channel tetramerization domain containing 8 148003 LGALS16 galectin 16 3960 LGALS4 galectin 4 653499 LGALS7B galectin 7B 80313 LRRC27 leucine rich repeat containing 27 10724 MGEA5 O-GlcNAcase 4820 NKTR natural killer cell triggering receptor 91662 NLRP12 NLR family pyrin domain containing 12 5027 P2RX7 purinergic receptor P2X 7 24145 PANX1 pannexin 1 56666 PANX2 pannexin 2 65018 PINK1 PTEN induced putative kinase 1 5481 PPID peptidylprolyl isomerase D 9360 PPIG peptidylprolyl isomerase G 10465 PPIH peptidylprolyl isomerase H 285755 PPIL6 peptidylprolyl isomerase like 6 118471 PRAP1 proline rich acidic protein 1 10728 PTGES3 prostaglandin E synthase 3 100885848 PTGES3L prostaglandin E synthase 3 like 100885850 PTGES3L-AARSD1 PTGES3L-AARSD1 readthrough 6013 RLN1 relaxin 1 91582 RPS19BP1 ribosomal protein S19 binding protein 1 6449 SGTA small glutamine rich tetratricopeptide repeat containing alpha 54557 SGTB small glutamine rich tetratricopeptide repeat containing beta 6493 SIM2 SIM bHLH transcription factor 2 6569 SLC34A1 solute carrier family 34 member 1 84189 SLITRK6 SLIT and NTRK like family member 6 6767 ST13 ST13, Hsp70 interacting protein 10963 STIP1 stress induced phosphoprotein 1 10910 SUGT1 SGT1 homolog, MIS12 kinetochore complex assembly cochaperone 283507 SUGT1P3 SUGT1 pseudogene 3 50945 TBX22 T-box 22 200424 TET3 tet methylcytosine dioxygenase 3 51078 THAP4 THAP domain containing 4 134288 TMEM174 transmembrane protein 174 203562 TMEM31 transmembrane protein 31 27242 TNFRSF21 TNF receptor superfamily member 21 7190 TRAP1 heat shock protein 90 beta family member 2, pseudogene 54970 TTC12 tetratricopeptide repeat domain 12 23331 TTC28 tetratricopeptide repeat domain 28 64427 TTC31 tetratricopeptide repeat domain 31 9889 ZBED4 zinc finger BED-type containing 4

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 2.22e-01 7.41e-05 GO methylcytosine dioxygenase activity molecular_function 1.79e-01 1.18e-18 Reactome Attenuation phase Cellular responses to external stimuli 1.14e-01 1.00e-07 Reactome The NLRP3 inflammasome Immune System 1.07e-01 1.48e-06 Reactome Aryl hydrocarbon receptor signalling Metabolism 7.41e-02 1.93e-08 GO cyclosporin A binding molecular_function 7.39e-02 1.23e-04 Reactome Electric Transmission Across Gap Junctions Neuronal System 6.68e-02 5.78e-11 GO Hsp90 protein binding molecular_function 6.35e-02 1.23e-04 Reactome Transmission across Electrical Synapses Neuronal System 5.06e-02 9.48e-17 Reactome HSF1 activation Cellular responses to external stimuli 4.32e-02 4.40e-04 GO posttranslational protein targeting to endoplasmic reticulum membrane biological_process 2.88e-02 1.88e-05 GO regulation of protein complex assembly biological_process 2.48e-02 4.58e-18 GO unfolded protein binding molecular_function 2.11e-02 1.06e-02 Reactome Type II Na+/Pi cotransporters Transport of small molecules 1.88e-02 6.68e-04 GO glycoprotein metabolic process biological_process 9.78e-03 7.19e-11 GO chaperone binding molecular_function 4.55e-03 2.07e-12 GO regulation of cellular response to heat biological_process 3.58e-03 9.44e-04 GO response to growth hormone biological_process 2.37e-03 4.24e-07 GO chaperone-mediated protein complex assembly biological_process 1.63e-03 9.44e-04 GO protein heterotrimerization biological_process 1.25e-03 1.53e-08 GO protein refolding 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 0.00e+00 0.00e+00 protein folding 1.02e-11 6.79e-09 unfolded protein binding 4.49e-10 2.52e-07 heat shock protein binding 1.31e-09 9.61e-07 regulation of cellular response to heat 5.52e-09 2.61e-06 chaperone binding 9.48e-09 6.18e-06 chaperone-mediated protein folding 3.46e-08 2.09e-05 protein refolding 4.24e-08 1.73e-05 cyclosporin A binding 3.27e-07 1.70e-04 telomerase holoenzyme complex assembly 1.22e-06 5.70e-04 chaperone cofactor-dependent protein refolding 1.66e-06 5.06e-04 peptidyl-prolyl cis-trans isomerase activity 3.28e-06 1.41e-03 protein peptidyl-prolyl isomerization 1.86e-05 4.61e-03 Hsp90 protein binding 2.47e-05 8.65e-03 DNA demethylation 2.89e-05 6.90e-03 ATPase regulator activity 3.64e-05 1.22e-02 regulation of cellular response to stress 4.07e-05 1.34e-02 protein oligomerization 4.45e-05 1.45e-02 regulation of protein stability 5.20e-05 1.17e-02 isomerase activity 5.78e-05 1.82e-02 telomere maintenance via telomerase

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 7.67e-07 1.35e-04 THE NLRP3 INFLAMMASOME 1.85e-06 3.09e-04 INFLAMMASOMES 1.89e-06 4.06e-04 THE NLRP3 INFLAMMASOME 6.73e-06 1.32e-03 INFLAMMASOMES 1.27e-04 1.93e-02 NUCLEOTIDE BINDING DOMAIN LEUCINE RICH REPEAT CONTAINING RECEPTOR NLR SIGNALING PATHWAYS 1.49e-04 1.82e-02 NUCLEOTIDE BINDING DOMAIN LEUCINE RICH REPEAT CONTAINING RECEPTOR NLR SIGNALING PATHWAYS 1.58e-04 2.33e-02 SEMA3A PAK DEPENDENT AXON REPULSION 4.23e-04 5.57e-02 SIGNALING BY CONSTITUTIVELY ACTIVE EGFR 4.85e-04 5.28e-02 SEMA3A PAK DEPENDENT AXON REPULSION 1.41e-03 1.36e-01 SIGNALING BY CONSTITUTIVELY ACTIVE EGFR 4.24e-03 3.99e-01 SEMAPHORIN INTERACTIONS 5.47e-03 4.41e-01 SEMAPHORIN INTERACTIONS 9.85e-03 7.24e-01 AXON GUIDANCE 1.10e-02 8.59e-01 AXON GUIDANCE 1.14e-02 8.84e-01 INNATE IMMUNE SYSTEM 1.20e-02 9.20e-01 SIGNALING BY ERBB2 1.25e-02 9.50e-01 NEURONAL SYSTEM 1.35e-02 1.00e+00 SIGNALING BY EGFR IN CANCER 1.46e-02 9.94e-01 INNATE IMMUNE SYSTEM 1.52e-02 1.00e+00 NEURONAL SYSTEM

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 2.73e-03 1e+00 decreased fibroblast proliferation 3.56e-03 1e+00 increased interleukin-10 secretion 3.64e-03 1e+00 abnormal neuron physiology 4.22e-03 1e+00 decreased birth weight 5.65e-03 1e+00 acoria 5.92e-03 1e+00 abnormal tooth development 7.48e-03 1e+00 decreased type II pneumocyte number 7.49e-03 1e+00 abnormal prostate gland development 8.74e-03 1e+00 decreased caudal vertebrae number 9.35e-03 1e+00 increased prolactinoma incidence 9.36e-03 1e+00 absent nasal bone 1.12e-02 1e+00 decreased palatal length 1.31e-02 1e+00 abnormal vomer bone morphology 1.31e-02 1e+00 tongue ankylosis 1.31e-02 1e+00 decreased trophoblast glycogen cell number 1.31e-02 1e+00 delayed suture closure 1.49e-02 1e+00 decreased diameter of long bones 1.49e-02 1e+00 abnormal nasopharynx morphology 1.49e-02 1e+00 abnormal placenta junctional zone morphology 1.61e-02 1e+00 intracranial hemorrhage

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

²FDR corrected p-value (Benjamini-Hochberg)