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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod106

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod106 Module size 34 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 2100 ESR2 estrogen receptor 2 2101 ESRRA estrogen related receptor alpha 2103 ESRRB estrogen related receptor beta 2104 ESRRG estrogen related receptor gamma 6927 HNF4A HNF1 homeobox A 3174 HNF4G hepatocyte nuclear factor 4 gamma 8431 NR0B2 nuclear receptor subfamily 0 group B member 2 9572 NR1D1 nuclear receptor subfamily 1 group D member 1 9975 NR1D2 nuclear receptor subfamily 1 group D member 2 7376 NR1H2 nuclear receptor subfamily 1 group H member 2 7181 NR2C1 nuclear receptor subfamily 2 group C member 1 7182 NR2C2 nuclear receptor subfamily 2 group C member 2 126382 NR2C2AP nuclear receptor 2C2 associated protein 7101 NR2E1 nuclear receptor subfamily 2 group E member 1 7025 NR2F1 nuclear receptor subfamily 2 group F member 1 2063 NR2F6 nuclear receptor subfamily 2 group F member 6 3164 NR4A1 nuclear receptor subfamily 4 group A member 1 4929 NR4A2 nuclear receptor subfamily 4 group A member 2 2516 NR5A1 nuclear receptor subfamily 5 group A member 1 29959 NRBP1 nuclear receptor binding protein 1 5241 PGR progesterone receptor 5467 PPARD peroxisome proliferator activated receptor delta 5914 RARA retinoic acid receptor alpha 5915 RARB retinoic acid receptor beta 5916 RARG retinoic acid receptor gamma 6095 RORA RAR related orphan receptor A 6096 RORB RAR related orphan receptor B 6097 RORC RAR related orphan receptor C 6256 RXRA retinoid X receptor alpha 6257 RXRB retinoid X receptor beta 6258 RXRG retinoid X receptor gamma 7067 THRA thyroid hormone receptor alpha 7068 THRB thyroid hormone receptor beta 1594 VDR cytochrome P450 family 27 subfamily B member 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 3.24e-01 4.64e-93 Reactome Nuclear Receptor transcription pathway Gene expression (Transcription) 1.99e-01 1.04e-85 GO steroid hormone receptor activity molecular_function 7.56e-02 6.17e-19 GO retinoic acid receptor signaling pathway biological_process 5.84e-02 7.01e-76 GO steroid hormone mediated signaling pathway biological_process 1.53e-02 2.43e-65 GO nuclear receptor 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 transcription initiation from RNA polymerase II promoter 0e+00 0e+00 hormone-mediated signaling pathway 0e+00 0e+00 response to hormone 0e+00 0e+00 cellular response to hormone stimulus 0e+00 0e+00 cellular response to organic cyclic compound 0e+00 0e+00 steroid hormone mediated signaling pathway 0e+00 0e+00 cellular response to lipid 0e+00 0e+00 intracellular receptor signaling pathway 0e+00 0e+00 DNA-templated transcription, initiation 0e+00 0e+00 response to steroid hormone 0e+00 0e+00 cellular response to steroid hormone stimulus 0e+00 0e+00 negative regulation of transcription from RNA polymerase II promoter 0e+00 0e+00 retinoic acid receptor signaling pathway 0e+00 0e+00 transcription regulatory region sequence-specific DNA binding 0e+00 0e+00 transcription factor activity, direct ligand regulated sequence-specific DNA binding 0e+00 0e+00 RNA polymerase II transcription factor activity, ligand-activated sequence-specific DNA binding 0e+00 0e+00 steroid hormone receptor activity 0e+00 0e+00 RNA polymerase II transcription factor activity, sequence-specific DNA binding 0e+00 0e+00 retinoic acid receptor 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 NUCLEAR RECEPTOR TRANSCRIPTION PATHWAY 0.00e+00 0.00e+00 GENERIC TRANSCRIPTION PATHWAY 0.00e+00 0.00e+00 NUCLEAR RECEPTOR TRANSCRIPTION PATHWAY 5.54e-05 7.39e-03 CIRCADIAN REPRESSION OF EXPRESSION BY REV ERBA 5.58e-05 7.44e-03 RORA ACTIVATES CIRCADIAN EXPRESSION 9.64e-05 1.23e-02 BMAL1 CLOCK NPAS2 ACTIVATES CIRCADIAN EXPRESSION 1.05e-04 1.62e-02 CIRCADIAN REPRESSION OF EXPRESSION BY REV ERBA 1.40e-04 1.72e-02 PPARA ACTIVATES GENE EXPRESSION 1.70e-04 2.05e-02 CIRCADIAN CLOCK 1.81e-04 2.63e-02 RORA ACTIVATES CIRCADIAN EXPRESSION 3.23e-04 3.66e-02 REGULATION OF GENE EXPRESSION IN BETA CELLS 5.03e-04 6.47e-02 BMAL1 CLOCK NPAS2 ACTIVATES CIRCADIAN EXPRESSION 1.40e-03 1.57e-01 CIRCADIAN CLOCK 1.53e-03 1.47e-01 FATTY ACID TRIACYLGLYCEROL AND KETONE BODY METABOLISM 2.15e-03 2.27e-01 PPARA ACTIVATES GENE EXPRESSION 2.76e-03 2.80e-01 REGULATION OF GENE EXPRESSION IN BETA CELLS 6.95e-03 5.97e-01 REGULATION OF BETA CELL DEVELOPMENT 8.38e-03 6.97e-01 FATTY ACID TRIACYLGLYCEROL AND KETONE BODY METABOLISM 1.24e-02 8.77e-01 SIGNALING BY ERBB4 2.79e-02 1.00e+00 REGULATION OF BETA CELL DEVELOPMENT

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 2.78e-05 9.81e-02 abnormal uterus physiology 5.86e-05 1.59e-01 fusion of atlas and odontoid process 1.13e-04 2.45e-01 split cervical atlas 1.13e-04 2.45e-01 split cervical axis 5.54e-04 6.46e-01 abnormal response to vitamins 1.17e-03 9.85e-01 increased triiodothyronine level 1.20e-03 1.00e+00 abnormal Purkinje cell differentiation 1.21e-03 1.00e+00 abnormal cricoid cartilage morphology 1.25e-03 1.00e+00 persistent hyperplastic primary vitreous 1.27e-03 1.00e+00 fusion of vertebral arches 1.48e-03 1.00e+00 fusion of atlas and occipital bones 1.77e-03 1.00e+00 abnormal hemoglobin 1.96e-03 1.00e+00 abnormal retinal inner plexiform layer morphology 2.06e-03 1.00e+00 cervical vertebral transformation 2.53e-03 1.00e+00 abnormal thyroid physiology 2.59e-03 1.00e+00 seminiferous tubule degeneration 2.68e-03 1.00e+00 abnormal cardiac cell glucose uptake 2.75e-03 1.00e+00 narrow eye opening 2.84e-03 1.00e+00 shortened circadian period 2.99e-03 1.00e+00 decreased circulating cholesterol level

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

²FDR corrected p-value (Benjamini-Hochberg)