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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod321

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod321 Module size 50 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 154796 AMOT angiomotin 154810 AMOTL1 angiomotin like 1 51421 AMOTL2 angiomotin like 2 22863 ATG14 autophagy related 14 9083 BPY2 basic charge Y-linked 2 442868 BPY2C basic charge Y-linked 2C 387856 C12orf68 coiled-coil domain containing 184 80178 C16orf59 tubulin epsilon and delta complex 2 51759 C9orf78 chromosome 9 open reading frame 78 165055 CCDC138 coiled-coil domain containing 138 317762 CCDC85C coiled-coil domain containing 85C 23109 DDN dendrin 9873 FCHSD2 FCH and double SH3 domains 2 9638 FEZ1 fasciculation and elongation protein zeta 1 9637 FEZ2 fasciculation and elongation protein zeta 2 79981 FRMD1 FERM domain containing 1 122786 FRMD6 FERM domain containing 6 4131 MAP1B microtubule associated protein 1B 55201 MAP1S microtubule associated protein 1S 6789 MST1 serine/threonine kinase 4 84224 NBPF3 NBPF member 3 4750 NEK1 NIMA related kinase 1 4771 NF2 neurofibromin 2 261734 NPHP4 nephrocystin 4 10081 PDCD7 programmed cell death 7 23368 PPP1R13B protein phosphatase 1 regulatory subunit 13B 22930 RAB3GAP1 RAB3 GTPase activating protein catalytic subunit 1 25782 RAB3GAP2 RAB3 GTPase activating non-catalytic protein subunit 2 11186 RASSF1 Ras association domain family member 1 9770 RASSF2 Ras association domain family member 2 83593 RASSF3 Ras association domain family member 5 54453 RASSF4 Ras and Rab interactor 2 166824 RASSF6 Ras association domain family member 6 8045 RASSF7 Ras association domain family member 7 11228 RASSF8 Ras association domain family member 8 9182 RASSF9 Ras association domain family member 9 64062 RBM26 RNA binding motif protein 26 89958 SAPCD2 suppressor APC domain containing 2 60485 SAV1 salvador family WW domain containing protein 1 60592 SCOC short coiled-coil protein 64663 SPANXC SPANX family member C 6704 SPRR2E small proline rich protein 2E 9333 TGM5 transglutaminase 5 7159 TP53BP2 tumor protein p53 binding protein 2 116461 TSEN15 tRNA splicing endonuclease subunit 15 80746 TSEN2 tRNA splicing endonuclease subunit 2 79042 TSEN34 tRNA splicing endonuclease subunit 34 283989 TSEN54 tRNA splicing endonuclease subunit 54 23335 WDR7 WD repeat domain 7 25937 WWTR1 WW domain containing transcription regulator 1

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 1.66e-01 2.94e-12 Reactome Signaling by Hippo Signal Transduction 1.44e-01 8.32e-07 GO tRNA splicing, via endonucleolytic cleavage and ligation biological_process 5.89e-02 1.32e-04 GO mitochondrion transport along microtubule biological_process 4.30e-02 1.70e-04 Reactome Activation of PUMA and translocation to mitochondria Programmed Cell Death 3.02e-02 7.97e-06 GO apical junction complex cellular_component 2.81e-02 6.62e-03 Reactome Signaling by MST1 Signal Transduction 2.01e-02 2.59e-04 GO positive regulation of autophagosome assembly biological_process 1.75e-02 2.12e-04 GO lyase activity molecular_function 1.17e-02 3.10e-04 GO negative regulation of autophagosome 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 3.58e-10 2.81e-07 hippo signaling 1.23e-09 6.43e-07 tRNA-intron endonuclease activity 1.58e-08 7.01e-06 endoribonuclease activity, producing 3'-phosphomonoesters 3.30e-08 2.00e-05 tRNA splicing, via endonucleolytic cleavage and ligation 1.94e-07 7.08e-05 tRNA-specific ribonuclease activity 2.14e-07 6.88e-05 tRNA-intron endonuclease complex 4.34e-07 2.20e-04 tRNA-type intron splice site recognition and cleavage 9.56e-07 4.56e-04 regulation of macroautophagy 2.31e-06 1.02e-03 regulation of autophagosome assembly 3.57e-06 9.48e-04 apical junction complex 3.70e-06 1.05e-03 endoribonuclease activity 6.44e-06 2.60e-03 regulation of vacuole organization 7.99e-06 3.16e-03 positive regulation of macroautophagy 1.44e-05 5.36e-03 establishment of mitochondrion localization 3.16e-05 7.02e-03 bicellular tight junction 3.19e-05 1.08e-02 RNA phosphodiester bond hydrolysis, endonucleolytic 4.22e-05 1.39e-02 regulation of autophagy 4.66e-05 1.06e-02 endonuclease activity 4.98e-05 1.13e-02 nuclease activity 5.53e-05 1.75e-02 regulation of protein complex stability

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 1.74e-11 5.04e-09 SIGNALING BY HIPPO 8.78e-03 7.21e-01 SMAD2 SMAD3 SMAD4 HETEROTRIMER REGULATES TRANSCRIPTION 1.62e-02 1.00e+00 SMAD2 SMAD3 SMAD4 HETEROTRIMER REGULATES TRANSCRIPTION 1.77e-02 1.00e+00 TRANSCRIPTIONAL ACTIVITY OF SMAD2 SMAD3 SMAD4 HETEROTRIMER 2.16e-02 1.00e+00 TRANSCRIPTIONAL ACTIVITY OF SMAD2 SMAD3 SMAD4 HETEROTRIMER 2.20e-02 1.00e+00 YAP1 AND WWTR1 TAZ STIMULATED GENE EXPRESSION 2.81e-02 1.00e+00 SIGNALING BY TGF BETA RECEPTOR COMPLEX 3.41e-02 1.00e+00 SIGNALING BY TGF BETA RECEPTOR COMPLEX 3.43e-02 1.00e+00 YAP1 AND WWTR1 TAZ STIMULATED GENE EXPRESSION 3.79e-02 1.00e+00 PPARA ACTIVATES GENE EXPRESSION

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 8.90e-05 2.10e-01 increased lymphoma incidence 5.69e-04 6.57e-01 abnormal renal tubule morphology 7.38e-04 7.59e-01 increased incidence of tumors by ionizing radiation induction 8.47e-04 8.20e-01 increased osteosarcoma incidence 1.86e-03 1.00e+00 abnormal retinal outer plexiform layer morphology 1.96e-03 1.00e+00 partial embryonic lethality between implantation and somite formation 2.81e-03 1.00e+00 abnormal keratinocyte differentiation 3.08e-03 1.00e+00 abnormal retinal outer nuclear layer morphology 3.38e-03 1.00e+00 overexpanded pulmonary alveoli 3.94e-03 1.00e+00 kidney cortex cysts 4.53e-03 1.00e+00 abnormal choroid plexus morphology 6.16e-03 1.00e+00 polycystic kidney 7.13e-03 1.00e+00 abnormal visceral endoderm morphology 7.81e-03 1.00e+00 epidermal hyperplasia 8.62e-03 1.00e+00 impaired skin barrier function 9.33e-03 1.00e+00 increased embryonic neuroepithelial cell proliferation 9.34e-03 1.00e+00 dermal hyperplasia 9.35e-03 1.00e+00 increased rhabdomyosarcoma incidence 1.09e-02 1.00e+00 abnormal olfactory bulb morphology 1.12e-02 1.00e+00 increased mesothelioma incidence

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

²FDR corrected p-value (Benjamini-Hochberg)