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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod121

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod121 Module size 32 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 2296 FOXC1 forkhead box C1 2303 FOXC2 forkhead box C2 2297 FOXD1 forkhead box D1 2306 FOXD2 forkhead box D2 27022 FOXD3 forkhead box D3 2298 FOXD4 forkhead box D4 200350 FOXD4L1 forkhead box D4 like 1 349334 FOXD4L2 forkhead box D4 like 4 286380 FOXD4L3 forkhead box D4 like 3 349334 FOXD4L4 forkhead box D4 like 4 653427 FOXD4L5 forkhead box D4 like 5 653404 FOXD4L6 forkhead box D4 like 6 2304 FOXE1 forkhead box E1 2301 FOXE3 forkhead box E3 2294 FOXF1 forkhead box F1 2295 FOXF2 forkhead box F2 2299 FOXI1 forkhead box I1 399823 FOXI2 forkhead box I2 2302 FOXJ1 forkhead box J1 55810 FOXJ2 forkhead box J2 22887 FOXJ3 forkhead box J3 2300 FOXL1 forkhead box L1 668 FOXL2 forkhead box L2 8456 FOXN1 forkhead box N1 3344 FOXN2 forkhead box N2 1112 FOXN3 forkhead box N3 121643 FOXN4 forkhead box N4 116113 FOXP4 forkhead box P4 94234 FOXQ1 forkhead box Q1 283150 FOXR1 forkhead box R1 139628 FOXR2 forkhead box R2 2307 FOXS1 forkhead box S1

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 1.24e-01 4.82e-11 GO DNA binding, bending molecular_function 1.04e-01 3.91e-36 GO anatomical structure 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 0.00e+00 0.00e+00 RNA polymerase II transcription factor activity, sequence-specific DNA binding 1.63e-10 9.72e-08 DNA binding, bending 1.40e-07 7.71e-05 transcription from RNA polymerase II promoter 4.54e-07 2.30e-04 tissue morphogenesis 9.73e-07 3.09e-04 transcription regulatory region DNA binding 1.02e-06 3.23e-04 regulatory region DNA binding 2.48e-06 7.29e-04 transcription regulatory region sequence-specific DNA binding 2.98e-06 8.64e-04 transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific binding 8.45e-06 3.33e-03 embryonic organ morphogenesis 8.78e-06 3.44e-03 embryonic organ development 9.02e-06 2.38e-03 double-stranded DNA binding 1.01e-05 3.90e-03 tube development 1.02e-05 2.66e-03 RNA polymerase II regulatory region sequence-specific DNA binding 1.03e-05 2.68e-03 RNA polymerase II regulatory region DNA binding 1.36e-05 5.09e-03 morphogenesis of an epithelium 3.86e-05 1.28e-02 embryonic morphogenesis 7.54e-05 2.29e-02 camera-type eye development 1.01e-04 2.94e-02 regulation of apoptotic process involved in outflow tract morphogenesis 1.15e-04 3.29e-02 negative regulation of transcription from RNA polymerase II promoter 1.31e-04 2.61e-02 transcription factor activity, RNA polymerase II distal enhancer sequence-specific binding

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 3.84e-06 2.36e-02 abnormal canal of Schlemm morphology 3.71e-05 1.17e-01 abnormal iridocorneal angle 8.98e-05 2.12e-01 aortic arch coarctation 1.24e-04 2.59e-01 abnormal trabecular meshwork morphology 1.60e-04 3.08e-01 abnormal iris pigment epithelium 1.78e-04 3.25e-01 abnormal hair cortex morphology 1.79e-04 3.26e-01 iris stroma hypoplasia 2.23e-04 3.73e-01 hypoplastic trabecular meshwork 3.51e-04 4.91e-01 ciliary body hypoplasia 3.60e-04 5.00e-01 abnormal soft palate morphology 4.43e-04 5.65e-01 abnormal palatine bone horizontal plate morphology 5.72e-04 6.58e-01 short ureter 6.31e-04 6.93e-01 small vertebral body 7.03e-04 7.37e-01 abnormal sphenoid bone morphology 7.39e-04 7.60e-01 abnormal hair shaft morphology 8.22e-04 8.04e-01 abnormal eye morphology 1.51e-03 1.00e+00 small basisphenoid bone 1.64e-03 1.00e+00 abnormal fourth pharyngeal arch artery morphology 2.05e-03 1.00e+00 anterior iris synechia 2.06e-03 1.00e+00 hydroureter

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

²FDR corrected p-value (Benjamini-Hochberg)