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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod146

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod146 Module size 27 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 254427 C10orf47 proline and serine rich 2 51719 CAB39 calcium binding protein 39 81617 CAB39L calcium binding protein 39 like 10129 FRY FRY microtubule binding protein 83855 KLF16 Kruppel like factor 16 9113 LATS1 large tumor suppressor kinase 1 26524 LATS2 large tumor suppressor kinase 2 79705 LRRK1 leucine rich repeat kinase 1 1326 MAP3K8 mitogen-activated protein kinase kinase kinase 8 11184 MAP4K1 mitogen-activated protein kinase kinase kinase kinase 1 5871 MAP4K2 mitogen-activated protein kinase kinase kinase kinase 2 8491 MAP4K3 mitogen-activated protein kinase kinase kinase kinase 3 11183 MAP4K5 mitogen-activated protein kinase kinase kinase kinase 5 55233 MOB1A MOB kinase activator 1A 92597 MOB1B MOB kinase activator 1B 81532 MOB2 MOB kinase activator 2 126308 MOB3A MOB kinase activator 3A 148932 MOB3C MOB kinase activator 3C 56980 PRDM10 PR/SET domain 10 114821 SCAND3 zinc finger BED-type containing 9 8428 STK24 serine/threonine kinase 24 10494 STK25 serine/threonine kinase 25 8428 STK3 serine/threonine kinase 24 11329 STK38 serine/threonine kinase 38 23012 STK38L serine/threonine kinase 38 like 6789 STK4 serine/threonine kinase 4 678 ZFP36L2 ZFP36 ring finger protein like 2

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 1.57e-01 1.09e-13 Reactome Signaling by Hippo Signal Transduction 1.43e-01 5.21e-14 GO activation of MAPKKK activity biological_process 8.33e-02 2.04e-22 GO signal transduction by protein 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 signal transducer, downstream of receptor, with serine/threonine kinase activity 0.00e+00 0.00e+00 protein kinase activity 0.00e+00 0.00e+00 signal transducer activity, downstream of receptor 0.00e+00 0.00e+00 protein serine/threonine kinase activity 0.00e+00 0.00e+00 phosphotransferase activity, alcohol group as acceptor 6.66e-11 5.63e-08 hippo signaling 1.38e-10 1.13e-07 signal transduction by protein phosphorylation 1.88e-10 1.11e-07 MAP kinase kinase kinase kinase activity 2.04e-10 1.64e-07 regulation of protein serine/threonine kinase activity 1.59e-08 1.01e-05 activation of MAPKKK activity 2.04e-08 1.28e-05 regulation of protein kinase activity 3.87e-08 2.32e-05 regulation of kinase activity 7.49e-07 3.65e-04 positive regulation of protein serine/threonine kinase activity 7.78e-07 3.78e-04 peptidyl-serine phosphorylation 9.85e-07 3.13e-04 magnesium ion binding 1.17e-06 5.49e-04 positive regulation of protein kinase activity 1.87e-06 8.44e-04 positive regulation of kinase activity 3.05e-06 1.32e-03 stress-activated MAPK cascade 3.71e-06 1.58e-03 stress-activated protein kinase signaling cascade 6.60e-06 1.78e-03 kinase activator activity

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 SIGNALING BY HIPPO 7.12e-10 1.77e-07 SIGNALING BY HIPPO 2.83e-04 3.89e-02 REGULATION OF AMPK ACTIVITY VIA LKB1 4.11e-04 5.43e-02 ENERGY DEPENDENT REGULATION OF MTOR BY LKB1 AMPK 5.54e-04 7.05e-02 ACTIVATED AMPK STIMULATES FATTY ACID OXIDATION IN MUSCLE 6.86e-04 8.46e-02 PKB MEDIATED EVENTS 1.04e-03 1.04e-01 REGULATION OF AMPK ACTIVITY VIA LKB1 1.05e-03 1.05e-01 ACTIVATED AMPK STIMULATES FATTY ACID OXIDATION IN MUSCLE 1.29e-03 1.26e-01 ENERGY DEPENDENT REGULATION OF MTOR BY LKB1 AMPK 1.70e-03 1.86e-01 PI3K CASCADE 1.87e-03 1.75e-01 PKB MEDIATED EVENTS 2.01e-03 2.14e-01 INSULIN RECEPTOR SIGNALLING CASCADE 3.22e-03 2.83e-01 PI3K CASCADE 3.44e-03 3.35e-01 CD28 DEPENDENT PI3K AKT SIGNALING 3.80e-03 3.25e-01 INSULIN RECEPTOR SIGNALLING CASCADE 6.88e-03 5.92e-01 CD28 CO STIMULATION 7.34e-03 6.25e-01 SIGNALING BY INSULIN RECEPTOR 7.74e-03 5.95e-01 SIGNALING BY INSULIN RECEPTOR 9.04e-03 6.76e-01 CD28 DEPENDENT PI3K AKT SIGNALING 1.09e-02 7.84e-01 CD28 CO STIMULATION

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 6.69e-04 7.19e-01 abnormal dendritic cell antigen presentation 7.03e-04 7.37e-01 increased T cell proliferation 3.74e-03 1.00e+00 abnormal marginal zone B cell morphology 4.64e-03 1.00e+00 abnormal mitosis 5.61e-03 1.00e+00 abnormal Peyer's patch T cell area morphology 5.61e-03 1.00e+00 delayed muscle development 5.61e-03 1.00e+00 adenohypophysis hyperplasia 7.47e-03 1.00e+00 decreased macrophage cytokine production 8.48e-03 1.00e+00 abnormal dendritic cell physiology 9.33e-03 1.00e+00 decreased myeloid dendritic cell number 9.33e-03 1.00e+00 increased cell nucleus count 1.12e-02 1.00e+00 abnormal enterocyte apoptosis 1.30e-02 1.00e+00 rectal hemorrhage 1.30e-02 1.00e+00 osteosclerosis 1.31e-02 1.00e+00 abnormal Peyer's patch germinal center morphology 1.51e-02 1.00e+00 abnormal cell morphology 1.86e-02 1.00e+00 abnormal bone marrow cavity morphology 1.86e-02 1.00e+00 abnormal fourth ventricle morphology 1.90e-02 1.00e+00 decreased IgG1 level 1.90e-02 1.00e+00 abnormal cytokine secretion

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

²FDR corrected p-value (Benjamini-Hochberg)