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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod89

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod89 Module size 49 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 8536 CAMK1 calcium/calmodulin dependent protein kinase I 57118 CAMK1D calcium/calmodulin dependent protein kinase ID 57172 CAMK1G calcium/calmodulin dependent protein kinase IG 814 CAMK4 calcium/calmodulin dependent protein kinase IV 8558 CDK10 cyclin dependent kinase 10 65061 CDK15 cyclin dependent kinase 15 5129 CDK18 cyclin dependent kinase 18 8814 CDKL1 cyclin dependent kinase like 1 8999 CDKL2 cyclin dependent kinase like 2 344387 CDKL4 cyclin dependent kinase like 4 23604 DAPK2 death associated protein kinase 2 1613 DAPK3 death associated protein kinase 3 51135 IRAK4 interleukin 1 receptor associated kinase 4 225689 MAPK15 mitogen-activated protein kinase 15 4342 MOS MOS proto-oncogene, serine/threonine kinase 340156 MYLK4 myosin light chain kinase family member 4 4752 NEK3 NIMA related kinase 3 10783 NEK6 NIMA related kinase 6 140609 NEK7 NIMA related kinase 7 9891 NUAK1 NUAK family kinase 1 81788 NUAK2 NUAK family kinase 2 9943 OXSR1 oxidative stress responsive 1 10298 PAK4 p21 (RAC1) activated kinase 4 149420 PDIK1L PDLIM1 interacting kinase 1 like 5292 PIM1 Pim-1 proto-oncogene, serine/threonine kinase 11040 PIM2 Pim-2 proto-oncogene, serine/threonine kinase 415116 PIM3 Pim-3 proto-oncogene, serine/threonine kinase 139728 PNCK pregnancy up-regulated nonubiquitous CaM kinase 5681 PSKH1 protein serine kinase H1 85481 PSKH2 protein serine kinase H2 6199 RPS6KB2 ribosomal protein S6 kinase B2 388228 SBK1 SH3 domain binding kinase 1 646643 SBK2 SH3 domain binding kinase family member 2 23678 SGK2 serum/glucocorticoid regulated kinase family member 3 23678 SGK3 serum/glucocorticoid regulated kinase family member 3 6794 STK11 serine/threonine kinase 11 8576 STK16 serine/threonine kinase 16 9263 STK17A serine/threonine kinase 17a 9262 STK17B serine/threonine kinase 17b 202374 STK32A serine/threonine kinase 32A 55351 STK32B serine/threonine kinase 32B 282974 STK32C serine/threonine kinase 32C 65975 STK33 serine/threonine kinase 33 83942 TSSK1B testis specific serine kinase 1B 23617 TSSK2 testis specific serine kinase 2 81629 TSSK3 testis specific serine kinase 3 83983 TSSK4 testis specific serine kinase 6 83983 TSSK6 testis specific serine kinase 6 25989 ULK3 unc-51 like kinase 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 9.42e-02 3.57e-09 GO calmodulin-dependent protein kinase activity molecular_function 7.48e-02 5.35e-03 Reactome Activation of CaMK IV Neuronal System 6.50e-02 5.74e-10 GO cyclin-dependent protein serine/threonine kinase activity molecular_function 4.50e-02 1.46e-04 Reactome Activation of NIMA Kinases NEK9, NEK6, NEK7 Cell Cycle 2.84e-02 3.11e-04 GO anoikis biological_process 2.49e-02 3.11e-04 GO regulation of cellular senescence biological_process 1.80e-02 3.11e-04 Reactome via Dependence Receptors in the absence of ligand Programmed Cell Death 1.25e-02 2.79e-06 GO regulation of mitotic cell cycle biological_process 2.69e-03 2.40e-09 GO peptidyl-serine phosphorylation 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 autophosphorylation 0.00e+00 0.00e+00 peptidyl-serine phosphorylation 0.00e+00 0.00e+00 peptidyl-threonine phosphorylation 0.00e+00 0.00e+00 protein kinase activity 0.00e+00 0.00e+00 protein serine/threonine kinase activity 0.00e+00 0.00e+00 phosphotransferase activity, alcohol group as acceptor 1.71e-09 8.73e-07 magnesium ion binding 1.29e-08 5.79e-06 cyclin-dependent protein serine/threonine kinase activity 1.77e-08 7.77e-06 cyclin-dependent protein kinase activity 2.02e-07 7.34e-05 calmodulin-dependent protein kinase activity 6.83e-06 1.84e-03 signal transducer, downstream of receptor, with serine/threonine kinase activity 3.63e-05 8.48e-03 calmodulin binding 4.41e-05 1.44e-02 regulation of mitotic cell cycle 6.00e-05 1.33e-02 signal transducer activity, downstream of receptor 8.40e-05 2.51e-02 anoikis 2.08e-04 5.41e-02 signal transduction by protein phosphorylation 2.69e-04 6.73e-02 positive regulation of fibroblast apoptotic process 4.57e-04 7.76e-02 chloride channel regulator activity 5.45e-04 1.20e-01 regulation of chromosome organization 5.54e-04 1.22e-01 positive regulation of CREB transcription factor activity

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 2.28e-04 2.67e-02 ROLE OF DCC IN REGULATING APOPTOSIS 4.62e-04 6.01e-02 ROLE OF DCC IN REGULATING APOPTOSIS 1.34e-02 9.30e-01 REGULATION OF APOPTOSIS 1.43e-02 1.00e+00 REGULATION OF APOPTOSIS 2.71e-02 1.00e+00 TRAF6 MEDIATED IRF7 ACTIVATION IN TLR7 8 OR 9 SIGNALING 2.85e-02 1.00e+00 TRAF6 MEDIATED IRF7 ACTIVATION IN TLR7 8 OR 9 SIGNALING 3.16e-02 1.00e+00 DOWNSTREAM SIGNAL TRANSDUCTION 3.58e-02 1.00e+00 ACTIVATION OF RAC 3.63e-02 1.00e+00 DOWNSTREAM SIGNAL TRANSDUCTION 3.64e-02 1.00e+00 SIGNALING BY ERBB2 3.75e-02 1.00e+00 APOPTOSIS 3.87e-02 1.00e+00 SIGNALING BY EGFR IN CANCER 3.88e-02 1.00e+00 REGULATION OF AMPK ACTIVITY VIA LKB1 3.88e-02 1.00e+00 ACTIVATION OF RAC 3.91e-02 1.00e+00 SIGNALING BY ERBB2 3.92e-02 1.00e+00 SIGNALING BY PDGF 4.04e-02 1.00e+00 DOWNSTREAM SIGNALING OF ACTIVATED FGFR 4.10e-02 1.00e+00 DOWNSTREAM SIGNALING OF ACTIVATED FGFR 4.35e-02 1.00e+00 SIGNALING BY EGFR IN CANCER 4.70e-02 1.00e+00 ENERGY DEPENDENT REGULATION OF MTOR BY LKB1 AMPK

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 7.46e-04 7.62e-01 increased intestinal adenoma incidence 3.77e-03 1.00e+00 absent first pharyngeal arch 3.99e-03 1.00e+00 abnormal sperm head morphology 5.34e-03 1.00e+00 abnormal placenta vasculature 7.48e-03 1.00e+00 thin hair shaft 7.50e-03 1.00e+00 accelerated hair follicle regression 7.52e-03 1.00e+00 increased endometrial carcinoma incidence 9.33e-03 1.00e+00 decreased interleukin-18 secretion 9.35e-03 1.00e+00 abnormal lung position or orientation 9.35e-03 1.00e+00 abnormal lung bud morphology 9.36e-03 1.00e+00 kinked vibrissae 1.11e-02 1.00e+00 partial lethality throughout fetal growth and development 1.13e-02 1.00e+00 increased hamartoma incidence 1.31e-02 1.00e+00 abnormal primary polar body morphology 1.31e-02 1.00e+00 decreased susceptibility to experimental autoimmune encephalomyelitis 1.31e-02 1.00e+00 abnormal hair follicle bulb morphology 1.31e-02 1.00e+00 abnormal hair follicle dermal papilla morphology 1.31e-02 1.00e+00 binucleate 1.49e-02 1.00e+00 increased teratoma incidence 1.49e-02 1.00e+00 delayed chorioallantoic fusion

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

²FDR corrected p-value (Benjamini-Hochberg)