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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod145

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod145 Module size 46 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 9370 ADIPOQ adiponectin, C1Q and collagen domain containing 51129 ANGPTL4 angiopoietin like 4 892 CCNC cyclin C 117106 CD36 scavenger receptor class B, member 2 1050 CEBPA CCAAT enhancer binding protein alpha 1051 CEBPB CCAAT enhancer binding protein beta 1052 CEBPD CCAAT enhancer binding protein delta 1879 EBF1 early B cell factor 1 2167 FABP4 fatty acid binding protein 4 84246 MED10 mediator complex subunit 10 400569 MED11 mediator complex subunit 11 9968 MED12 mediator complex subunit 12 116931 MED12L mediator complex subunit 12 like 9969 MED13 mediator complex subunit 13 23389 MED13L mediator complex subunit 13 like 9282 MED14 mediator complex subunit 14 51586 MED15 mediator complex subunit 15 10025 MED16 mediator complex subunit 16 9440 MED17 mediator complex subunit 17 54797 MED18 mediator complex subunit 18 219541 MED19 mediator complex subunit 19 9477 MED20 mediator complex subunit 20 9412 MED21 mediator complex subunit 21 6837 MED22 mediator complex subunit 22 9439 MED23 mediator complex subunit 23 9862 MED24 mediator complex subunit 24 81857 MED25 mediator complex subunit 25 9441 MED26 mediator complex subunit 26 9442 MED27 mediator complex subunit 27 80306 MED28 mediator complex subunit 28 55588 MED29 mediator complex subunit 29 90390 MED30 mediator complex subunit 30 51003 MED31 mediator complex subunit 31 29079 MED4 mediator complex subunit 4 10001 MED6 mediator complex subunit 6 9443 MED7 mediator complex subunit 7 112950 MED8 mediator complex subunit 8 55090 MED9 mediator complex subunit 9 8202 NCOA3 nuclear receptor coactivator 3 9612 NCOR2 nuclear receptor corepressor 2 5346 PLIN1 perilipin 1 10891 PPARGC1A PPARG coactivator 1 alpha 133522 PPARGC1B PPARG coactivator 1 beta 10432 RBM14 RNA binding motif protein 14 100526737 RBM14-RBM4 RBM14-RBM4 readthrough 9967 THRAP3 thyroid hormone receptor associated protein 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 4.01e-01 2.63e-108 Reactome Transcriptional regulation of white adipocyte differentiation Developmental Biology 3.75e-01 1.70e-80 GO mediator complex cellular_component 1.96e-02 1.56e-44 GO transcription coregulator activity molecular_function

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 transcription from RNA polymerase II promoter 0e+00 0e+00 DNA-templated transcription, initiation 0e+00 0e+00 transcription initiation from RNA polymerase II promoter 0e+00 0e+00 response to steroid hormone 0e+00 0e+00 steroid hormone mediated signaling pathway 0e+00 0e+00 hormone-mediated signaling pathway 0e+00 0e+00 cellular response to steroid hormone stimulus 0e+00 0e+00 intracellular steroid hormone receptor signaling pathway 0e+00 0e+00 cellular response to lipid 0e+00 0e+00 androgen receptor signaling pathway 0e+00 0e+00 cellular response to organic cyclic compound 0e+00 0e+00 intracellular receptor signaling pathway 0e+00 0e+00 mediator complex 0e+00 0e+00 core mediator complex 0e+00 0e+00 transcription factor activity, RNA polymerase II transcription factor binding 0e+00 0e+00 transcription cofactor activity 0e+00 0e+00 transcription coactivator activity 0e+00 0e+00 transcription factor activity, transcription factor binding 0e+00 0e+00 transcription factor activity, protein binding 0e+00 0e+00 RNA polymerase II transcription cofactor 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 TRANSCRIPTIONAL REGULATION OF WHITE ADIPOCYTE DIFFERENTIATION 0.00e+00 0.00e+00 DEVELOPMENTAL BIOLOGY 0.00e+00 0.00e+00 PPARA ACTIVATES GENE EXPRESSION 0.00e+00 0.00e+00 FATTY ACID TRIACYLGLYCEROL AND KETONE BODY METABOLISM 0.00e+00 0.00e+00 GENERIC TRANSCRIPTION PATHWAY 0.00e+00 0.00e+00 TRANSCRIPTIONAL REGULATION OF WHITE ADIPOCYTE DIFFERENTIATION 0.00e+00 0.00e+00 PPARA ACTIVATES GENE EXPRESSION 0.00e+00 0.00e+00 FATTY ACID TRIACYLGLYCEROL AND KETONE BODY METABOLISM 1.50e-03 1.67e-01 HORMONE SENSITIVE LIPASE HSL MEDIATED TRIACYLGLYCEROL HYDROLYSIS 2.58e-03 2.33e-01 HORMONE SENSITIVE LIPASE HSL MEDIATED TRIACYLGLYCEROL HYDROLYSIS 3.94e-03 3.75e-01 CIRCADIAN REPRESSION OF EXPRESSION BY REV ERBA 3.95e-03 3.76e-01 RORA ACTIVATES CIRCADIAN EXPRESSION 5.17e-03 4.22e-01 CIRCADIAN REPRESSION OF EXPRESSION BY REV ERBA 5.18e-03 4.23e-01 RORA ACTIVATES CIRCADIAN EXPRESSION 1.31e-02 9.85e-01 TRANSCRIPTIONAL ACTIVITY OF SMAD2 SMAD3 SMAD4 HETEROTRIMER 1.31e-02 9.12e-01 BMAL1 CLOCK NPAS2 ACTIVATES CIRCADIAN EXPRESSION 1.33e-02 9.97e-01 BMAL1 CLOCK NPAS2 ACTIVATES CIRCADIAN EXPRESSION 1.71e-02 1.00e+00 CIRCADIAN CLOCK 2.23e-02 1.00e+00 CIRCADIAN CLOCK 3.10e-02 1.00e+00 TRANSCRIPTIONAL ACTIVITY OF SMAD2 SMAD3 SMAD4 HETEROTRIMER

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 5.53e-07 5.68e-03 abnormal gluconeogenesis 1.53e-06 1.19e-02 abnormal brown adipose tissue morphology 5.83e-06 3.22e-02 abnormal glucose homeostasis 2.22e-05 8.24e-02 decreased triglyceride level 3.89e-05 1.21e-01 abnormal hormone level 4.31e-05 1.29e-01 impaired adaptive thermogenesis 4.33e-05 1.29e-01 increased liver triglyceride level 7.91e-05 1.94e-01 abnormal lipid homeostasis 9.47e-05 2.18e-01 abnormal cell differentiation 9.86e-05 2.24e-01 impaired lipolysis 1.68e-04 3.15e-01 abnormal white adipose tissue morphology 2.59e-04 4.09e-01 decreased oxygen consumption 5.38e-04 6.35e-01 insulin resistance 5.47e-04 6.42e-01 abnormal B cell morphology 6.85e-04 7.28e-01 decreased circulating triglyceride level 8.61e-04 8.28e-01 increased erythroid progenitor cell number 1.11e-03 9.56e-01 hypoglycemia 1.30e-03 1.00e+00 decreased white fat cell size 1.30e-03 1.00e+00 abnormal fat cell morphology 1.32e-03 1.00e+00 decreased adiponectin level

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

²FDR corrected p-value (Benjamini-Hochberg)