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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod314

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod314 Module size 42 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 421 ARVCF ARVCF, delta catenin family member 22926 ATF6 activating transcription factor 6 1388 ATF6B activating transcription factor 6 beta 162681 C18orf54 chromosome 18 open reading frame 54 55561 CDC42BPG CDC42 binding protein kinase gamma 1496 CTNNA2 catenin alpha 2 29119 CTNNA3 catenin alpha 3 1501 CTNND2 catenin delta 2 51473 DCDC2 doublecortin domain containing 2 149069 DCDC2B doublecortin domain containing 2B 728597 DCDC2C doublecortin domain containing 2C 54798 DCHS2 dachsous cadherin-related 2 291130 DCX doublecortin domain containing 2 1825 DSC1 desmocollin 3 1825 DSC2 desmocollin 3 1828 DSG1 desmoglein 1 1829 DSG2 desmoglein 2 388650 FAM69A family with sequence similarity 69 member A 2196 FAT2 FAT atypical cadherin 2 79633 FAT4 FAT atypical cadherin 4 2844 GPR21 G protein-coupled receptor 21 8994 LIMD1 LIM domains containing 1 4026 LPP LIM domain containing preferred translocation partner in lipoma 92312 MEX3A mex-3 RNA binding family member A 9722 NOS1AP nitric oxide synthase 1 adaptor protein 10038 PARP2 poly(ADP-ribose) polymerase 2 10039 PARP3 poly(ADP-ribose) polymerase family member 3 5317 PKP1 plakophilin 1 5318 PKP2 plakophilin 2 11187 PKP3 plakophilin 3 8502 PKP4 plakophilin 4 5365 PLXNB3 plexin B3 266697 POM121L4P POM121 transmembrane nucleoporin like 4, pseudogene 29942 PURG purine rich element binding protein G 94137 RP1L1 RP1 like 1 80176 SPSB1 splA/ryanodine receptor domain and SOCS box containing 1 92369 SPSB4 splA/ryanodine receptor domain and SOCS box containing 4 7205 TRIP6 thyroid hormone receptor interactor 6 10497 UNC13B unc-13 homolog B 126374 WTIP WT1 interacting protein 463 ZFHX3 zinc finger homeobox 3 79776 ZFHX4 zinc finger homeobox 4

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 1.61e-01 2.17e-16 GO desmosome cellular_component 1.11e-01 5.95e-09 GO regulation of ventricular cardiac muscle cell action potential biological_process 5.91e-02 1.25e-04 GO protein poly-ADP-ribosylation biological_process 5.53e-02 1.25e-04 GO negative regulation of hippo signaling biological_process 5.36e-02 1.09e-06 GO messenger ribonucleoprotein complex cellular_component 4.56e-02 4.27e-12 GO cell-cell junction assembly biological_process 4.11e-02 1.61e-04 GO ATF6-mediated unfolded protein response biological_process 7.28e-03 5.27e-13 GO cell-cell adherens junction cellular_component 7.02e-03 2.45e-04 GO gene silencing by miRNA biological_process 4.05e-03 2.45e-04 GO positive regulation of transcription from RNA polymerase II promoter in response to endoplasmic reticulum stress biological_process 1.03e-03 2.45e-04 GO positive regulation of gene silencing by miRNA biological_process 3.69e-04 8.59e-13 GO cell-cell junction cellular_component

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 single organismal cell-cell adhesion 0.00e+00 0.00e+00 cell-cell adhesion 0.00e+00 0.00e+00 cornified envelope 0.00e+00 0.00e+00 desmosome 1.97e-11 1.75e-08 cornification 2.88e-11 1.85e-08 protein binding involved in cell-cell adhesion 9.67e-11 8.04e-08 keratinization 1.31e-10 1.07e-07 regulation of ventricular cardiac muscle cell action potential 1.61e-10 8.08e-08 cell-cell junction 3.73e-10 2.13e-07 cell adhesive protein binding involved in bundle of His cell-Purkinje myocyte communication 9.68e-10 7.23e-07 keratinocyte differentiation 1.51e-09 1.10e-06 cell-cell adhesion via plasma-membrane adhesion molecules 1.95e-09 9.89e-07 protein binding involved in heterotypic cell-cell adhesion 2.65e-09 1.87e-06 homophilic cell adhesion via plasma membrane adhesion molecules 3.67e-09 2.53e-06 regulation of cardiac muscle cell action potential 3.91e-09 2.68e-06 bundle of His cell-Purkinje myocyte adhesion involved in cell communication 4.66e-09 3.17e-06 epidermal cell differentiation 6.62e-09 4.40e-06 cardiac muscle cell-cardiac muscle cell adhesion 9.43e-09 6.16e-06 regulation of cardiac muscle cell contraction 4.43e-08 2.64e-05 regulation of action potential

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 1.26e-06 2.81e-04 APOPTOTIC CLEAVAGE OF CELL ADHESION PROTEINS 6.35e-06 9.81e-04 APOPTOTIC CLEAVAGE OF CELL ADHESION PROTEINS 1.87e-05 3.40e-03 APOPTOTIC CLEAVAGE OF CELLULAR PROTEINS 4.32e-05 7.34e-03 APOPTOTIC EXECUTION PHASE 5.99e-05 7.93e-03 APOPTOTIC CLEAVAGE OF CELLULAR PROTEINS 8.68e-05 1.12e-02 APOPTOTIC EXECUTION PHASE 1.82e-04 2.64e-02 APOPTOSIS 4.66e-04 5.09e-02 APOPTOSIS 7.22e-03 5.62e-01 ACTIVATION OF CHAPERONE GENES BY ATF6 ALPHA 8.89e-03 6.68e-01 ACTIVATION OF CHAPERONES BY ATF6 ALPHA 1.00e-02 7.32e-01 GLUTAMATE NEUROTRANSMITTER RELEASE CYCLE 1.03e-02 8.15e-01 ACTIVATION OF CHAPERONE GENES BY ATF6 ALPHA 1.24e-02 9.44e-01 ACTIVATION OF CHAPERONES BY ATF6 ALPHA 1.47e-02 1.00e+00 OTHER SEMAPHORIN INTERACTIONS 2.36e-02 1.00e+00 ACTIVATION OF GENES BY ATF4 2.44e-02 1.00e+00 PERK REGULATED GENE EXPRESSION 2.52e-02 1.00e+00 ACTIVATION OF GENES BY ATF4 2.68e-02 1.00e+00 PERK REGULATED GENE EXPRESSION 2.85e-02 1.00e+00 ANTIGEN PROCESSING UBIQUITINATION PROTEASOME DEGRADATION 2.85e-02 1.00e+00 OTHER SEMAPHORIN INTERACTIONS

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 3.56e-04 4.95e-01 parakeratosis 1.73e-03 1.00e+00 disheveled coat 1.87e-03 1.00e+00 acantholysis 2.54e-03 1.00e+00 epidermal hyperplasia 2.56e-03 1.00e+00 abnormal epidermal layer morphology 2.80e-03 1.00e+00 dermatitis 3.35e-03 1.00e+00 thick epidermis 4.52e-03 1.00e+00 increased sensitivity to induced cell death 5.27e-03 1.00e+00 abnormal vertebrae morphology 5.61e-03 1.00e+00 abnormal osteoclast cell number 6.41e-03 1.00e+00 abnormal cell death 7.48e-03 1.00e+00 increased keratinocyte apoptosis 7.48e-03 1.00e+00 abnormal epidermis stratum spinosum morphology 7.48e-03 1.00e+00 ectopic hippocampus pyramidal cells 7.61e-03 1.00e+00 abnormal cued conditioning behavior 7.98e-03 1.00e+00 abnormal spatial learning 8.27e-03 1.00e+00 alopecia 9.34e-03 1.00e+00 decreased kidney cell proliferation 9.34e-03 1.00e+00 abnormal circulating serum amyloid protein level 9.35e-03 1.00e+00 abnormal circulating chemokine level

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

²FDR corrected p-value (Benjamini-Hochberg)