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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod71

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod71 Module size 58 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 80823 BHLHB9 basic helix-loop-helix family member b9 55259 CASC1 cancer susceptibility 1 255919 CNEP1R1 CTD nuclear envelope phosphatase 1 regulatory subunit 1 64651 CSRNP1 cysteine and serine rich nuclear protein 1 81566 CSRNP2 cysteine and serine rich nuclear protein 2 80034 CSRNP3 cysteine and serine rich nuclear protein 3 23399 CTDNEP1 CTD nuclear envelope phosphatase 1 22873 DZIP1 DAZ interacting zinc finger protein 1 8870 IER3 immediate early response 3 51278 IER5 immediate early response 5 51451 LCMT1 leucine carboxyl methyltransferase 1 9836 LCMT2 leucine carboxyl methyltransferase 2 22853 LMTK2 lemur tyrosine kinase 2 114783 LMTK3 lemur tyrosine kinase 3 5499 PPP1CA protein phosphatase 1 catalytic subunit alpha 5500 PPP1CB protein phosphatase 1 catalytic subunit beta 5514 PPP1R10 protein phosphatase 1 regulatory subunit 10 4659 PPP1R12A protein phosphatase 1 regulatory subunit 12A 84919 PPP1R15B protein phosphatase 1 regulatory subunit 15B 10842 PPP1R17 protein phosphatase 1 regulatory subunit 17 5502 PPP1R1A protein phosphatase 1 regulatory inhibitor subunit 1A 84152 PPP1R1B protein phosphatase 1 regulatory inhibitor subunit 1B 220004 PPP1R32 protein phosphatase 1 regulatory subunit 32 221908 PPP1R35 protein phosphatase 1 regulatory subunit 35 145376 PPP1R36 protein phosphatase 1 regulatory subunit 36 79660 PPP1R3B protein phosphatase 1 regulatory subunit 3B 89801 PPP1R3F protein phosphatase 1 regulatory subunit 3F 648791 PPP1R3G protein phosphatase 1 regulatory subunit 3G 55607 PPP1R9A protein phosphatase 1 regulatory subunit 9A 5515 PPP2CA protein phosphatase 2 catalytic subunit alpha 5516 PPP2CB protein phosphatase 2 catalytic subunit beta 5519 PPP2R1B protein phosphatase 2 scaffold subunit Abeta 5521 PPP2R2B protein phosphatase 2 regulatory subunit Bbeta 5522 PPP2R2C protein phosphatase 2 regulatory subunit Bgamma 55844 PPP2R2D protein phosphatase 2 regulatory subunit Bdelta 5523 PPP2R3A protein phosphatase 2 regulatory subunit B''alpha 28227 PPP2R3B protein phosphatase 2 regulatory subunit B''beta 5524 PPP2R4 protein phosphatase 2 phosphatase activator 5525 PPP2R5A protein phosphatase 2 regulatory subunit B'alpha 5526 PPP2R5B protein phosphatase 2 regulatory subunit B'beta 5527 PPP2R5C protein phosphatase 2 regulatory subunit B'gamma 5528 PPP2R5D protein phosphatase 2 regulatory subunit B'delta 5529 PPP2R5E protein phosphatase 2 regulatory subunit B'epsilon 9989 PPP4R1 protein phosphatase 4 regulatory subunit 1 55370 PPP4R1L protein phosphatase 4 regulatory subunit 1 like (pseudogene) 297486 PPP4R2 protein phosphatase 4, regulatory subunit 2 57718 PPP4R4 protein phosphatase 4 regulatory subunit 4 6262 RYR2 ryanodine receptor 2 8036 SHOC2 SHOC2, leucine rich repeat scaffold protein 50651 SLC45A1 solute carrier family 45 member 1 55671 SMEK1 protein phosphatase 4 regulatory subunit 3A 57223 SMEK2 protein phosphatase 4 regulatory subunit 3B 92293 TMEM132C transmembrane protein 132C 121256 TMEM132D transmembrane protein 132D 338661 TMEM225 transmembrane protein 225 9878 TOX4 TOX high mobility group box family member 4 286262 TPRN taperin 140831 ZSWIM3 zinc finger SWIM-type containing 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 2.83e-01 2.51e-31 GO protein phosphatase type 2A complex cellular_component 2.52e-01 3.48e-38 GO protein phosphatase regulator activity molecular_function 1.87e-01 5.20e-11 GO protein phosphatase type 1 complex cellular_component 7.16e-02 1.20e-15 GO peptidyl-serine dephosphorylation biological_process 5.55e-02 1.39e-10 GO negative regulation of phosphatase activity biological_process 2.54e-02 9.56e-17 Reactome Platelet sensitization by LDL Hemostasis 2.01e-02 1.19e-17 Reactome AXIN mutants destabilize the destruction complex, activating WNT signaling Disease 1.72e-02 1.65e-12 GO negative regulation of phosphoprotein phosphatase activity biological_process 1.67e-02 1.19e-17 Reactome AXIN missense mutants destabilize the destruction complex Disease 1.58e-02 1.19e-17 Reactome Truncations of AMER1 destabilize the destruction complex Disease 1.27e-02 3.30e-21 GO protein serine/threonine phosphatase activity molecular_function 1.15e-02 1.19e-17 Reactome truncated APC mutants destabilize the destruction complex Disease 1.11e-02 1.19e-17 Reactome APC truncation mutants have impaired AXIN binding Disease 1.08e-02 5.82e-04 GO mitotic nuclear envelope disassembly biological_process 9.24e-03 5.82e-04 GO positive regulation of triglyceride biosynthetic process biological_process 7.69e-03 3.60e-07 GO phosphatase binding molecular_function 6.82e-03 1.19e-17 Reactome AMER1 mutants destabilize the destruction complex Disease 4.63e-03 4.66e-23 GO protein dephosphorylation 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 regulation of phosphatase activity 0.00e+00 0.00e+00 regulation of dephosphorylation 0.00e+00 0.00e+00 protein dephosphorylation 0.00e+00 0.00e+00 dephosphorylation 0.00e+00 0.00e+00 protein serine/threonine phosphatase complex 0.00e+00 0.00e+00 protein phosphatase type 2A complex 0.00e+00 0.00e+00 phosphatase binding 0.00e+00 0.00e+00 phosphatase regulator activity 0.00e+00 0.00e+00 protein phosphatase regulator activity 0.00e+00 0.00e+00 protein serine/threonine phosphatase activity 0.00e+00 0.00e+00 phosphoprotein phosphatase activity 0.00e+00 0.00e+00 phosphatase activity 7.62e-12 6.89e-09 negative regulation of phosphatase activity 2.02e-11 1.11e-08 PTW/PP1 phosphatase complex 2.65e-11 2.32e-08 negative regulation of dephosphorylation 2.45e-10 1.43e-07 protein phosphatase inhibitor activity 2.75e-10 1.60e-07 phosphatase inhibitor activity 3.26e-10 1.88e-07 phosphoric ester hydrolase activity 1.35e-09 5.97e-07 protein phosphatase type 1 complex 7.58e-09 5.00e-06 regulation of glycogen biosynthetic process

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 0.00e+00 0.00e+00 CTLA4 INHIBITORY SIGNALING 0.00e+00 0.00e+00 PLATELET SENSITIZATION BY LDL 0.00e+00 0.00e+00 CTNNB1 PHOSPHORYLATION CASCADE 0.00e+00 0.00e+00 CTLA4 INHIBITORY SIGNALING 0.00e+00 0.00e+00 PLATELET SENSITIZATION BY LDL 0.00e+00 0.00e+00 CTNNB1 PHOSPHORYLATION CASCADE 6.59e-11 1.83e-08 MITOTIC PROMETAPHASE 2.33e-10 8.18e-08 MITOTIC PROMETAPHASE 3.45e-10 8.91e-08 PLATELET HOMEOSTASIS 6.92e-10 1.72e-07 COSTIMULATION BY THE CD28 FAMILY 1.82e-09 4.31e-07 DARPP 32 EVENTS 2.60e-09 6.05e-07 SIGNALING BY WNT 3.14e-09 9.67e-07 PLATELET HOMEOSTASIS 4.93e-09 1.49e-06 COSTIMULATION BY THE CD28 FAMILY 1.01e-08 2.96e-06 DARPP 32 EVENTS 1.45e-08 4.16e-06 SIGNALING BY WNT 1.81e-07 3.43e-05 GLYCOLYSIS 5.40e-07 9.84e-05 MITOTIC M M G1 PHASES 8.82e-07 1.55e-04 INHIBITION OF REPLICATION INITIATION OF DAMAGED DNA BY RB1 E2F1 1.05e-06 2.37e-04 INHIBITION OF REPLICATION INITIATION OF DAMAGED DNA BY RB1 E2F1

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 5.56e-04 6.46e-01 enhanced behavioral response to cocaine 1.54e-03 1.00e+00 heart left ventricle hypertrophy 2.43e-03 1.00e+00 abnormal physiological response to xenobiotic 3.74e-03 1.00e+00 ventricular fibrillation 5.83e-03 1.00e+00 decreased cardiac muscle contractility 7.48e-03 1.00e+00 abnormal primordial germ cell morphology 7.48e-03 1.00e+00 ventricular premature beat 7.48e-03 1.00e+00 echinocytosis 7.48e-03 1.00e+00 abnormal tumor necrosis factor secretion 8.65e-03 1.00e+00 abnormal neuron physiology 1.12e-02 1.00e+00 abnormal head fold morphology 1.30e-02 1.00e+00 hyperactivity elicited by ethanol administration 1.30e-02 1.00e+00 atrial fibrillation 1.31e-02 1.00e+00 abnormal extraembryonic coelom morphology 1.31e-02 1.00e+00 abnormal extraembryonic mesoderm development 1.31e-02 1.00e+00 thin interventricular septum 1.31e-02 1.00e+00 decreased palatine bone horizontal plate size 1.49e-02 1.00e+00 abnormal presphenoid bone morphology 1.59e-02 1.00e+00 reduced long term potentiation 1.68e-02 1.00e+00 impaired behavioral response to morphine

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

²FDR corrected p-value (Benjamini-Hochberg)