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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod129

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod129 Module size 59 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 8092 ALX1 ALX homeobox 1 257 ALX3 ALX homeobox 3 60529 ALX4 ALX homeobox 4 10054 ARX ubiquitin like modifier activating enzyme 2 343472 BARHL2 BarH like homeobox 2 120237 DBX1 developing brain homeobox 1 440097 DBX2 developing brain homeobox 2 127343 DMBX1 diencephalon/mesencephalon homeobox 1 503834 DPRX divergent-paired related homeobox 644168 DRGX dorsal root ganglia homeobox 80712 ESX1 ESX homeobox 1 9247 GCM2 glial cells missing homolog 2 145258 GSC goosecoid homeobox 2928 GSC2 goosecoid homeobox 2 8820 HESX1 HESX homeobox 1 84525 HOPX HOP homeobox 26160 IFT172 intraflagellar transport 172 26525 IL36RN interleukin 36 receptor antagonist 3670 ISL1 ISL LIM homeobox 1 64843 ISL2 ISL LIM homeobox 2 91464 ISX intestine specific homeobox 10660 LBX1 ladybird homeobox 1 85474 LBX2 ladybird homeobox 2 9079 LDB1 LIM domain binding 2 9079 LDB2 LIM domain binding 2 3975 LHX1 LIM homeobox 1 9355 LHX2 LIM homeobox 2 8022 LHX3 LIM homeobox 3 89884 LHX4 LIM homeobox 4 64211 LHX5 LIM homeobox 5 26468 LHX6 LIM homeobox 6 431707 LHX8 LIM homeobox 8 56956 LHX9 LIM homeobox 9 4004 LMO1 LIM domain only 1 4005 LMO2 LIM domain only 2 55885 LMO3 LIM domain only 3 8543 LMO4 LIM domain only 4 4009 LMX1A LIM homeobox transcription factor 1 alpha 4010 LMX1B LIM homeobox transcription factor 1 beta 390010 NKX1-2 NK1 homeobox 2 135935 NOBOX NOBOX oogenesis homeobox 23440 OTP orthopedia homeobox 5015 OTX2 orthodenticle homeobox 2 5626 PROP1 PROP paired-like homeobox 1 5396 PRRX1 paired related homeobox 1 51450 PRRX2 paired related homeobox 2 30062 RAX retina and anterior neural fold homeobox 84839 RAX2 retina and anterior neural fold homeobox 2 158800 RHOXF1 Rhox homeobox family member 1 84528 RHOXF2 Rhox homeobox family member 2 727940 RHOXF2B Rhox homeobox family member 2B 645832 SEBOX SEBOX homeobox 6473 SHOX short stature homeobox 6474 SHOX2 short stature homeobox 2 23635 SSBP2 single stranded DNA binding protein 2 23648 SSBP3 single stranded DNA binding protein 3 170463 SSBP4 single stranded DNA binding protein 4 340260 UNCX UNC homeobox 118472 ZNF511 zinc finger protein 511

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 1.19e-01 4.10e-08 GO spinal cord association neuron differentiation biological_process 1.05e-01 1.81e-06 GO cerebellar Purkinje cell differentiation biological_process 1.02e-01 7.80e-08 GO spinal cord motor neuron differentiation biological_process 6.20e-02 1.66e-04 GO LIM domain binding molecular_function 5.35e-02 1.18e-08 GO dorsal/ventral pattern formation biological_process 4.29e-02 2.83e-04 GO dorsal spinal cord development biological_process 2.56e-02 3.54e-04 GO transcriptional repressor activity, RNA polymerase II distal enhancer sequence-specific binding molecular_function 2.33e-02 1.19e-05 GO motor neuron axon guidance biological_process 1.91e-02 2.05e-05 GO dopaminergic neuron differentiation biological_process 1.09e-02 3.60e-06 GO hair follicle development biological_process 8.00e-03 3.23e-05 GO regulation of hematopoietic stem cell differentiation biological_process 4.35e-03 1.15e-08 GO transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific DNA binding molecular_function 3.25e-03 2.40e-05 GO enhancer sequence-specific DNA 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 0.00e+00 0.00e+00 head development 0.00e+00 0.00e+00 transcription from RNA polymerase II promoter 0.00e+00 0.00e+00 forebrain development 0.00e+00 0.00e+00 pattern specification process 0.00e+00 0.00e+00 brain development 0.00e+00 0.00e+00 dorsal spinal cord development 0.00e+00 0.00e+00 spinal cord development 0.00e+00 0.00e+00 central nervous system neuron differentiation 0.00e+00 0.00e+00 cell differentiation in spinal cord 0.00e+00 0.00e+00 ventral spinal cord development 0.00e+00 0.00e+00 transcription factor complex 0.00e+00 0.00e+00 double-stranded DNA binding 0.00e+00 0.00e+00 RNA polymerase II regulatory region sequence-specific DNA binding 0.00e+00 0.00e+00 transcription regulatory region DNA binding 0.00e+00 0.00e+00 transcription regulatory region sequence-specific DNA binding 0.00e+00 0.00e+00 regulatory region DNA binding 0.00e+00 0.00e+00 RNA polymerase II transcription factor activity, sequence-specific DNA binding 0.00e+00 0.00e+00 RNA polymerase II regulatory region DNA binding 5.13e-11 4.39e-08 spinal cord motor neuron differentiation 2.50e-10 1.46e-07 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)

Reactome

P-value1 FDR2 Term 1.21e-03 1.39e-01 SYNTHESIS SECRETION AND INACTIVATION OF GIP 2.42e-03 2.51e-01 INCRETIN SYNTHESIS SECRETION AND INACTIVATION 3.25e-03 3.22e-01 REGULATION OF INSULIN SECRETION 7.05e-03 6.04e-01 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 1.57e-06 1.20e-02 abnormal midbrain-hindbrain boundary development 3.94e-06 2.42e-02 abnormal Rathke's pouch development 1.32e-05 5.70e-02 absent forebrain 4.03e-05 1.24e-01 absent midbrain 1.23e-04 2.59e-01 decreased gonadotroph cell number 1.36e-04 2.79e-01 abnormal head development 1.41e-04 2.85e-01 small adenohypophysis 1.64e-04 3.12e-01 abnormal malleus morphology 2.84e-04 4.36e-01 abnormal alisphenoid bone morphology 2.93e-04 4.42e-01 abnormal brain development 3.27e-04 4.72e-01 acephaly 3.28e-04 4.72e-01 absent hippocampal fimbria 3.71e-04 5.10e-01 embryonic-extraembryonic boundary constriction 4.37e-04 5.60e-01 abnormal neural tube morphology/development 4.52e-04 5.70e-01 abnormal temporomandibular joint morphology 4.52e-04 5.70e-01 abnormal rhombomere 3 morphology 4.95e-04 6.03e-01 abnormal craniofacial morphology 4.98e-04 6.04e-01 absent prechordal mesoderm 5.00e-04 6.05e-01 abnormal pretectal region morphology 5.04e-04 6.07e-01 abnormal neurohypophysis morphology

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

²FDR corrected p-value (Benjamini-Hochberg)