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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod38

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod38 Module size 61 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 1747 DLX3 distal-less homeobox 3 2128 EVX1 even-skipped homeobox 1 344191 EVX2 even-skipped homeobox 2 2636 GBX1 gastrulation brain homeobox 1 2637 GBX2 gastrulation brain homeobox 2 219409 GSX1 GS homeobox 1 170825 GSX2 GS homeobox 2 3206 HOXA10 homeobox A10 3207 HOXA11 homeobox A11 3209 HOXA13 homeobox A13 3199 HOXA2 homeobox A2 3200 HOXA3 homeobox A3 3201 HOXA4 homeobox A4 3202 HOXA5 homeobox A5 3211 HOXB1 homeobox B1 10481 HOXB13 homeobox B13 3212 HOXB2 homeobox B2 3213 HOXB3 homeobox B3 3214 HOXB4 homeobox B4 3215 HOXB5 homeobox B5 3216 HOXB6 homeobox B6 3217 HOXB7 homeobox B7 3218 HOXB8 homeobox B8 3219 HOXB9 homeobox B9 3226 HOXC10 homeobox C10 3227 HOXC11 homeobox C11 3228 HOXC12 homeobox C12 3229 HOXC13 homeobox C13 3221 HOXC4 homeobox C4 3222 HOXC5 homeobox C5 3223 HOXC6 homeobox C6 3224 HOXC8 homeobox C8 3225 HOXC9 homeobox C9 3231 HOXD1 homeobox D1 3236 HOXD10 homeobox D10 3237 HOXD11 homeobox D11 3238 HOXD12 homeobox D12 3239 HOXD13 homeobox D13 3232 HOXD3 homeobox D3 3233 HOXD4 homeobox D4 3234 HOXD8 homeobox D8 3235 HOXD9 homeobox D9 79192 IRX1 iroquois homeobox 1 153572 IRX2 iroquois homeobox 2 10265 IRX5 iroquois homeobox 5 55180 LINS lines homolog 1 4211 MEIS1 Meis homeobox 1 4212 MEIS2 Meis homeobox 2 56917 MEIS3 Meis homeobox 3 4222 MEOX1 mesenchyme homeobox 1 3110 MNX1 motor neuron and pancreas homeobox 1 5087 PBX1 PBX homeobox 1 5089 PBX2 PBX homeobox 2 5090 PBX3 PBX homeobox 3 80714 PBX4 PBX homeobox 4 267004 PGBD3 piggyBac transposable element derived 3 10745 PHTF1 putative homeodomain transcription factor 1 5316 PKNOX1 PBX/knotted 1 homeobox 1 90316 TGIF2LX TGFB induced factor homeobox 2 like X-linked 90655 TGIF2LY TGFB induced factor homeobox 2 like Y-linked 3195 TLX1 T cell leukemia homeobox 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 1.84e-01 6.59e-52 GO anterior/posterior pattern specification biological_process 1.76e-01 9.90e-33 GO embryonic skeletal system morphogenesis biological_process 1.21e-01 3.07e-15 GO proximal/distal pattern formation biological_process 2.65e-02 9.01e-21 Reactome Activation of HOX genes during differentiation Developmental Biology 2.50e-02 9.01e-21 Reactome Activation of anterior HOX genes in hindbrain development during early embryogenesis Developmental Biology 9.94e-03 3.77e-17 GO transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific DNA binding molecular_function 9.03e-03 4.46e-08 GO embryonic skeletal system development biological_process 7.04e-03 7.68e-04 GO regulation of respiratory gaseous exchange by neurological system process biological_process 5.81e-03 3.57e-04 GO dorsal spinal cord development biological_process 1.16e-03 7.45e-11 GO transcription factor activity, RNA polymerase II distal enhancer sequence-specific binding 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 chordate embryonic development 0e+00 0e+00 embryo development ending in birth or egg hatching 0e+00 0e+00 anterior/posterior pattern specification 0e+00 0e+00 embryonic organ morphogenesis 0e+00 0e+00 skeletal system development 0e+00 0e+00 pattern specification process 0e+00 0e+00 embryonic skeletal system development 0e+00 0e+00 skeletal system morphogenesis 0e+00 0e+00 embryonic skeletal system morphogenesis 0e+00 0e+00 embryonic morphogenesis 0e+00 0e+00 embryonic limb morphogenesis 0e+00 0e+00 limb development 0e+00 0e+00 limb morphogenesis 0e+00 0e+00 proximal/distal pattern formation 0e+00 0e+00 double-stranded DNA binding 0e+00 0e+00 RNA polymerase II regulatory region sequence-specific DNA binding 0e+00 0e+00 transcription regulatory region DNA binding 0e+00 0e+00 transcription regulatory region sequence-specific DNA binding 0e+00 0e+00 regulatory region DNA binding 0e+00 0e+00 transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific binding

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 0.00e+00 0.00e+00 cervical vertebral transformation 0.00e+00 0.00e+00 thoracic vertebral transformation 3.63e-10 1.62e-05 increased rib number 1.60e-08 3.55e-04 lumbar vertebral transformation 2.37e-08 4.75e-04 abnormal carpal bone morphology 6.44e-08 1.02e-03 sacral vertebral transformation 1.95e-07 2.45e-03 abnormal cervical vertebrae morphology 2.99e-06 2.00e-02 asymmetric rib-sternum attachment 5.70e-06 3.17e-02 short metacarpal bones 5.88e-06 3.23e-02 decreased sternebra number 1.37e-05 5.77e-02 abnormal rib-sternum attachment 2.38e-05 8.77e-02 increased sternebra number 2.57e-05 9.29e-02 caudal vertebral transformation 4.18e-05 1.28e-01 abnormal phalanx morphology 4.55e-05 1.34e-01 abnormal thoracic vertebrae morphology 5.46e-05 1.52e-01 abnormal hyoid bone lesser horn morphology 8.11e-05 1.98e-01 fusion of glossopharyngeal and vagus nerve 9.93e-05 2.25e-01 abnormal styloid process morphology 1.20e-04 2.54e-01 abnormal spinal nerve morphology 1.52e-04 2.97e-01 sacral vertebral fusion

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

²FDR corrected p-value (Benjamini-Hochberg)