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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod364

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod364 Module size 55 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 5243 ABCB1 ATP binding cassette subfamily B member 1 442867 BPY2B basic charge Y-linked 2B 10591 C6orf108 2'-deoxynucleoside 5'-phosphate N-hydrolase 1 4267 CD99 CD99 molecule (Xg blood group) 9696 CROCC ciliary rootlet coiled-coil, rootletin 81501 DCSTAMP dendrocyte expressed seven transmembrane protein 9909 DENND4B DENN domain containing 4B 9681 DEPDC5 DEP domain containing 5 1676 DFFA DNA fragmentation factor subunit alpha 9451 EIF2AK3 eukaryotic translation initiation factor 2 alpha kinase 3 11124 FAF1 Fas associated factor 1 23196 FAM120A family with sequence similarity 120A 2352 FOLR3 folate receptor 3 79443 FYCO1 FYVE and coiled-coil domain containing 1 51608 GET4 golgi to ER traffic protein 4 79618 HMBOX1 homeobox containing 1 23210 JMJD6 jumonji domain containing 6, arginine demethylase and lysine hydroxylase 57221 KIAA1244 ARFGEF family member 3 9209 LRRFIP2 LRR binding FLII interacting protein 2 4081 MAB21L1 mab-21 like 1 9476 NAPSA napsin A aspartic peptidase 4681 NBL1 NBL1, DAN family BMP antagonist 29881 NPC1L1 NPC1 like intracellular cholesterol transporter 1 81572 PDRG1 p53 and DNA damage regulated 1 284098 PIGW phosphatidylinositol glycan anchor biosynthesis class W 5300 PIN1 peptidylprolyl cis/trans isomerase, NIMA-interacting 1 27039 PKD2L2 polycystin 2 like 2, transient receptor potential cation channel 5612 PRKRIR THAP domain containing 12 7916 PRRC2A proline rich coiled-coil 2A 9698 PUM1 pumilio RNA binding family member 1 117584 RFFL ring finger and FYVE like domain containing E3 ubiquitin protein ligase 55658 RNF126 ring finger protein 126 165918 RNF168 ring finger protein 168 169166 SNX31 sorting nexin 31 147323 STARD6 StAR related lipid transfer domain containing 6 728929 TCEB3CL elongin A3 family member B 100506888 TCEB3CL2 elongin A3 family member D 22980 TCF25 transcription factor 25 146691 TOM1L2 target of myb1 like 2 membrane trafficking protein 9881 TRANK1 tetratricopeptide repeat and ankyrin repeat containing 1 117854 TRIM6 tripartite motif containing 6 7257 TSNAX translin associated factor X 55815 TSNAXIP1 translin associated factor X interacting protein 1 55236 UBA6 ubiquitin like modifier activating enzyme 6 54926 UBE2R2 ubiquitin conjugating enzyme E2 R2 7335 UBE2V1 ubiquitin conjugating enzyme E2 V1 26043 UBXN7 UBX domain protein 7 219333 USP12 ubiquitin specific peptidase 12 360471 USP7 ubiquitin specific peptidase 7 9101 USP8 ubiquitin specific peptidase 8 55717 WDR11 WD repeat domain 11 55841 WWC3 WWC family member 3 100132596 XG XG pseudogene, Y-linked 2 23039 XPO7 exportin 7 57688 ZSWIM6 zinc finger SWIM-type containing 6

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 4.41e-01 2.45e-03 Reactome Intestinal lipid absorption Digestion and absorption 3.03e-02 2.59e-04 GO VCP-NPL4-UFD1 AAA ATPase complex cellular_component 2.77e-02 7.32e-03 GO BAT3 complex cellular_component 2.31e-03 5.27e-05 Reactome Synthesis of active ubiquitin: roles of E1 and E2 enzymes Metabolism of proteins

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 9.31e-07 4.46e-04 protein catabolic process 6.85e-06 2.75e-03 ubiquitin-dependent protein catabolic process 8.09e-06 3.20e-03 modification-dependent protein catabolic process 2.04e-05 7.30e-03 proteolysis involved in cellular protein catabolic process 2.62e-05 9.11e-03 cellular protein catabolic process 1.20e-04 3.41e-02 protein polyubiquitination 1.91e-04 5.04e-02 protein K63-linked ubiquitination 1.91e-04 3.63e-02 ubiquitin protein ligase binding 2.17e-04 4.05e-02 ubiquitin-like protein ligase binding 2.31e-04 5.92e-02 negative regulation of execution phase of apoptosis 3.48e-04 5.90e-02 VCP-NPL4-UFD1 AAA ATPase complex 4.46e-04 7.60e-02 ubiquitin protein ligase activity 5.53e-04 1.21e-01 protein K48-linked ubiquitination 5.55e-04 1.22e-01 protein monoubiquitination 6.22e-04 1.34e-01 protein ubiquitination 1.26e-03 2.38e-01 regulation of execution phase of apoptosis 1.51e-03 2.76e-01 protein modification by small protein conjugation 1.97e-03 2.78e-01 peptidyl-lysine 5-dioxygenase activity 2.64e-03 3.58e-01 ubiquitin-protein transferase activity 2.73e-03 3.69e-01 thiol-dependent ubiquitin-specific protease activity

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 4.63e-03 3.85e-01 DOWNREGULATION OF ERBB2 ERBB3 SIGNALING 1.01e-02 8.06e-01 DOWNREGULATION OF ERBB2 ERBB3 SIGNALING 1.36e-02 9.40e-01 SIGNALING BY ERBB2 1.42e-02 9.73e-01 PERK REGULATED GENE EXPRESSION 1.43e-02 9.78e-01 ABACAVIR TRANSPORT AND METABOLISM 1.58e-02 1.00e+00 ABACAVIR TRANSPORT AND METABOLISM 1.97e-02 1.00e+00 SYNTHESIS OF GLYCOSYLPHOSPHATIDYLINOSITOL GPI 2.69e-02 1.00e+00 SIGNALING BY ERBB2 2.97e-02 1.00e+00 APOPTOSIS INDUCED DNA FRAGMENTATION 3.05e-02 1.00e+00 APOPTOSIS INDUCED DNA FRAGMENTATION 3.38e-02 1.00e+00 NEGATIVE REGULATORS OF RIG I MDA5 SIGNALING 4.18e-02 1.00e+00 POST TRANSLATIONAL MODIFICATION SYNTHESIS OF GPI ANCHORED PROTEINS 4.67e-02 1.00e+00 ANTIVIRAL MECHANISM BY IFN STIMULATED GENES 4.82e-02 1.00e+00 NEGATIVE REGULATORS OF RIG I MDA5 SIGNALING

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 3.75e-03 1e+00 absent lens vesicle 5.63e-03 1e+00 abnormal T cell receptor delta chain V(D)J recombination 5.63e-03 1e+00 aniridia 7.49e-03 1e+00 increased prostate gland tumor incidence 7.74e-03 1e+00 complete embryonic lethality 9.08e-03 1e+00 abnormal apoptosis 9.34e-03 1e+00 increased basal cell carcinoma incidence 9.34e-03 1e+00 abnormal optic placode morphology 1.12e-02 1e+00 abnormal primordial germ cell proliferation 1.12e-02 1e+00 exocrine pancreatic insufficiency 1.12e-02 1e+00 increased total retina thickness 1.12e-02 1e+00 abnormal CD8 positive, alpha-beta intraepithelial T cell morphology 1.12e-02 1e+00 catalepsy 1.14e-02 1e+00 reduced male fertility 1.26e-02 1e+00 abnormal cornea morphology 1.31e-02 1e+00 abnormal gallbladder morphology 1.31e-02 1e+00 abnormal male preputial gland morphology 1.47e-02 1e+00 increased physiological sensitivity to xenobiotic 1.49e-02 1e+00 absent pancreatic beta cells 1.49e-02 1e+00 abnormal circulating LDL cholesterol level

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

²FDR corrected p-value (Benjamini-Hochberg)