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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod133

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod133 Module size 36 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 1602 DACH1 dachshund family transcription factor 1 117154 DACH2 dachshund family transcription factor 2 1745 DLX1 distal-less homeobox 1 1748 DLX4 distal-less homeobox 4 1750 DLX6 distal-less homeobox 6 22947 DUX4 double homeobox 4 like 1 728410 DUX4L2 double homeobox 4 like 2 653548 DUX4L3 double homeobox 4 like 3 441056 DUX4L4 double homeobox 4 like 4 653545 DUX4L5 double homeobox 4 like 5 653544 DUX4L6 double homeobox 4 like 6 653543 DUX4L7 double homeobox 4 like 7 503835 DUXA double homeobox A 57593 EBF4 early B cell factor 4 2138 EYA1 EYA transcriptional coactivator and phosphatase 1 2139 EYA2 EYA transcriptional coactivator and phosphatase 2 2140 EYA3 EYA transcriptional coactivator and phosphatase 3 2070 EYA4 EYA transcriptional coactivator and phosphatase 4 3166 HMX1 H6 family homeobox 1 83881 MIXL1 Mix paired-like homeobox 5077 PAX3 paired box 3 5078 PAX4 paired box 4 5080 PAX6 paired box 6 5081 PAX7 paired box 7 6495 SIX1 SIX homeobox 1 10736 SIX2 SIX homeobox 2 6496 SIX3 SIX homeobox 3 51804 SIX4 SIX homeobox 4 147912 SIX5 SIX homeobox 5 4990 SIX6 SIX homeobox 6 9095 TBX19 T-box 19 6909 TBX2 T-box 2 9496 TBX4 T-box 4 11023 VAX1 ventral anterior homeobox 1 25806 VAX2 ventral anterior homeobox 2 338917 VSX2 visual system homeobox 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 3.15e-01 1.96e-24 GO anatomical structure development biological_process 2.20e-01 8.45e-11 GO histone dephosphorylation biological_process 3.47e-02 2.01e-13 GO transcriptional activator activity, RNA polymerase II distal enhancer sequence-specific DNA binding molecular_function 3.10e-02 1.14e-04 GO RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding molecular_function 2.15e-02 1.40e-04 GO transcription factor activity, RNA polymerase II core promoter sequence-specific binding involved in preinitiation complex assembly molecular_function 1.33e-02 1.67e-04 GO embryonic camera-type eye morphogenesis biological_process 6.65e-03 1.40e-06 GO aorta morphogenesis 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 3.81e-10 2.17e-07 RNA polymerase II transcription factor activity, sequence-specific DNA binding 3.99e-10 3.11e-07 sensory organ development 5.59e-10 4.29e-07 histone dephosphorylation 9.16e-10 4.90e-07 transcription regulatory region sequence-specific DNA binding 3.90e-09 1.89e-06 double-stranded DNA binding 6.15e-09 2.88e-06 transcription regulatory region DNA binding 6.18e-09 2.90e-06 regulatory region DNA binding 2.56e-08 1.58e-05 cell fate commitment 4.26e-08 1.74e-05 RNA polymerase II regulatory region sequence-specific DNA binding 4.36e-08 1.78e-05 RNA polymerase II regulatory region DNA binding 9.13e-08 5.19e-05 visual perception 1.04e-07 5.86e-05 sensory perception of light stimulus 3.65e-07 1.88e-04 embryonic morphogenesis 1.75e-06 7.95e-04 embryonic skeletal system development 1.84e-06 8.32e-04 neuron fate commitment 2.74e-06 1.19e-03 embryonic organ morphogenesis 2.81e-06 1.22e-03 mesodermal cell fate specification 4.09e-06 1.72e-03 negative regulation of extrinsic apoptotic signaling pathway in absence of ligand 4.12e-06 1.73e-03 positive regulation of DNA repair 4.19e-06 1.76e-03 eye development

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 3.44e-03 3.35e-01 REGULATION OF GENE EXPRESSION IN BETA CELLS 5.05e-03 4.61e-01 REGULATION OF BETA CELL DEVELOPMENT 1.37e-02 1.00e+00 SYNTHESIS SECRETION AND INACTIVATION OF GIP 1.37e-02 1.00e+00 SYNTHESIS SECRETION AND INACTIVATION OF GLP1 1.37e-02 1.00e+00 INCRETIN SYNTHESIS SECRETION AND INACTIVATION 2.98e-02 1.00e+00 REGULATION OF INSULIN SECRETION 3.82e-02 1.00e+00 INTEGRATION OF ENERGY METABOLISM

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 4.24e-06 2.56e-02 short endolymphatic duct 1.28e-05 5.64e-02 abnormal tympanic membrane morphology 2.18e-05 8.13e-02 coloboma 2.74e-05 9.75e-02 abnormal endolymphatic duct morphology 3.06e-05 1.04e-01 conductive hearing loss 8.23e-05 2.00e-01 decreased cochlear coiling 1.12e-04 2.44e-01 absent optic chiasm 1.62e-04 3.10e-01 thin diaphragm muscle 1.71e-04 3.19e-01 hypopigmentation 1.96e-04 3.45e-01 abnormal cardiovascular development 2.11e-04 3.59e-01 abnormal otic vesicle development 2.30e-04 3.79e-01 abnormal stapes morphology 2.65e-04 4.15e-01 abnormal vestibular saccule morphology 2.78e-04 4.31e-01 abnormal facial nerve morphology 3.21e-04 4.69e-01 absent inner ear 3.83e-04 5.20e-01 abnormal neural fold elevation formation 3.85e-04 5.21e-01 absent inner ear vestibule 4.02e-04 5.34e-01 abnormal middle ear morphology 4.31e-04 5.55e-01 absent stapedial artery 4.47e-04 5.68e-01 abnormal semicircular canal morphology

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

²FDR corrected p-value (Benjamini-Hochberg)