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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod52

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod52 Module size 36 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 338599 DUPD1 dual specificity phosphatase and pro isomerase domain containing 1 11221 DUSP10 dual specificity phosphatase 10 11266 DUSP12 dual specificity phosphatase 12 51207 DUSP13 dual specificity phosphatase 13 11072 DUSP14 dual specificity phosphatase 14 128853 DUSP15 dual specificity phosphatase 15 80824 DUSP16 dual specificity phosphatase 16 150290 DUSP18 dual specificity phosphatase 18 142679 DUSP19 dual specificity phosphatase 19 1844 DUSP2 dual specificity phosphatase 2 63904 DUSP21 dual specificity phosphatase 21 56940 DUSP22 dual specificity phosphatase 22 78986 DUSP26 dual specificity phosphatase 26 92235 DUSP27 dual specificity phosphatase 27, atypical 285193 DUSP28 dual specificity phosphatase 28 1845 DUSP3 dual specificity phosphatase 3 1846 DUSP4 dual specificity phosphatase 4 1847 DUSP5 dual specificity phosphatase 5 1848 DUSP6 dual specificity phosphatase 6 1849 DUSP7 dual specificity phosphatase 7 1850 DUSP8 dual specificity phosphatase 8 1852 DUSP9 dual specificity phosphatase 9 284131 ENDOV endonuclease V 7957 EPM2A EPM2A, laforin glucan phosphatase 5784 PTPN14 protein tyrosine phosphatase, non-receptor type 14 26095 PTPN20B protein tyrosine phosphatase, non-receptor type 20 5774 PTPN3 protein tyrosine phosphatase, non-receptor type 3 5775 PTPN4 protein tyrosine phosphatase, non-receptor type 4 84867 PTPN5 protein tyrosine phosphatase, non-receptor type 5 5778 PTPN7 protein tyrosine phosphatase, non-receptor type 7 54434 SSH1 slingshot protein phosphatase 1 85464 SSH2 slingshot protein phosphatase 2 54961 SSH3 slingshot protein phosphatase 3 6815 STYX serine/threonine/tyrosine interacting protein 51657 STYXL1 serine/threonine/tyrosine interacting like 1 55092 TMEM51 transmembrane protein 51

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 3.65e-01 5.19e-33 GO MAP kinase tyrosine/serine/threonine phosphatase activity molecular_function 3.08e-01 2.86e-59 GO protein tyrosine/serine/threonine phosphatase activity molecular_function 6.57e-02 2.76e-33 GO inactivation of MAPK activity biological_process 4.17e-02 1.01e-59 GO protein tyrosine phosphatase activity molecular_function 4.00e-02 7.48e-08 Reactome Interleukin-37 signaling Immune System 2.09e-02 1.22e-40 GO protein dephosphorylation biological_process 1.78e-03 2.00e-06 GO regulation of lamellipodium assembly 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 0e+00 0e+00 regulation of kinase activity 0e+00 0e+00 regulation of MAP kinase activity 0e+00 0e+00 regulation of MAPK cascade 0e+00 0e+00 negative regulation of MAP kinase activity 0e+00 0e+00 regulation of protein kinase activity 0e+00 0e+00 negative regulation of MAPK cascade 0e+00 0e+00 protein dephosphorylation 0e+00 0e+00 negative regulation of intracellular signal transduction 0e+00 0e+00 negative regulation of protein kinase activity 0e+00 0e+00 negative regulation of phosphorylation 0e+00 0e+00 inactivation of MAPK activity 0e+00 0e+00 negative regulation of protein phosphorylation 0e+00 0e+00 negative regulation of kinase activity 0e+00 0e+00 dephosphorylation 0e+00 0e+00 negative regulation of protein serine/threonine kinase activity 0e+00 0e+00 peptidyl-tyrosine dephosphorylation 0e+00 0e+00 regulation of protein serine/threonine kinase activity 0e+00 0e+00 hydrolase activity, acting on ester bonds 0e+00 0e+00 phosphoprotein phosphatase activity 0e+00 0e+00 MAP kinase phosphatase activity

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 8.98e-09 2.65e-06 ERKS ARE INACTIVATED 1.16e-08 3.37e-06 ERK MAPK TARGETS 2.94e-08 8.15e-06 NUCLEAR EVENTS KINASE AND TRANSCRIPTION FACTOR ACTIVATION 3.11e-08 8.59e-06 MAPK TARGETS NUCLEAR EVENTS MEDIATED BY MAP KINASES 1.19e-07 2.30e-05 ERKS ARE INACTIVATED 1.77e-07 4.45e-05 NGF SIGNALLING VIA TRKA FROM THE PLASMA MEMBRANE 2.20e-07 5.46e-05 MAP KINASE ACTIVATION IN TLR CASCADE 1.36e-06 2.31e-04 ERK MAPK TARGETS 1.57e-06 3.43e-04 TRAF6 MEDIATED INDUCTION OF NFKB AND MAP KINASES UPON TLR7 8 OR 9 ACTIVATION 2.37e-06 3.88e-04 NUCLEAR EVENTS KINASE AND TRANSCRIPTION FACTOR ACTIVATION 2.74e-06 5.71e-04 NFKB AND MAP KINASES ACTIVATION MEDIATED BY TLR4 SIGNALING REPERTOIRE 3.90e-06 7.94e-04 MYD88 MAL CASCADE INITIATED ON PLASMA MEMBRANE 4.18e-06 8.46e-04 TRIF MEDIATED TLR3 SIGNALING 5.17e-06 8.11e-04 MAPK TARGETS NUCLEAR EVENTS MEDIATED BY MAP KINASES 1.58e-05 2.92e-03 ACTIVATED TLR4 SIGNALLING 2.85e-05 5.02e-03 TOLL RECEPTOR CASCADES 3.21e-05 4.43e-03 MAP KINASE ACTIVATION IN TLR CASCADE 4.51e-05 7.63e-03 SIGNALLING BY NGF 9.46e-05 1.21e-02 NFKB AND MAP KINASES ACTIVATION MEDIATED BY TLR4 SIGNALING REPERTOIRE 1.07e-04 1.35e-02 TRAF6 MEDIATED INDUCTION OF NFKB AND MAP KINASES UPON TLR7 8 OR 9 ACTIVATION

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 2.86e-03 1e+00 increased tumor necrosis factor secretion 3.74e-03 1e+00 periorbital edema 5.31e-03 1e+00 abnormal cardiac cell glucose uptake 5.61e-03 1e+00 abnormal otic capsule morphology 5.61e-03 1e+00 heart hyperplasia 7.47e-03 1e+00 lymphatic vessel hyperplasia 9.34e-03 1e+00 decreased B cell apoptosis 1.12e-02 1e+00 abnormal long bone epiphyseal ossification zone morphology 1.12e-02 1e+00 premature suture closure 1.12e-02 1e+00 enlarged hippocampus 1.30e-02 1e+00 lymphedema 1.30e-02 1e+00 abnormal deltoid tuberosity morphology 1.31e-02 1e+00 hippocampal neuron degeneration 1.42e-02 1e+00 abnormal cytokine secretion 1.49e-02 1e+00 abnormal germ cell morphology 1.49e-02 1e+00 abnormal macrophage activation involved in immune response 1.65e-02 1e+00 increased liver cholesterol level 1.67e-02 1e+00 abnormal eye blink conditioning behavior 1.68e-02 1e+00 abnormal adaptive immunity 1.68e-02 1e+00 increased interleukin-10 secretion

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

²FDR corrected p-value (Benjamini-Hochberg)