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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod334

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod334 Module size 59 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 80325 ABTB1 ankyrin repeat and BTB domain containing 1 54882 ANKHD1 ankyrin repeat and KH domain containing 1 404734 ANKHD1-EIF4EBP3 ANKHD1-EIF4EBP3 readthrough 55608 ANKRD10 ankyrin repeat domain 10 26057 ANKRD17 ankyrin repeat domain 17 253650 ANKRD18A ankyrin repeat domain 18A 441459 ANKRD18B ankyrin repeat domain 18B 84210 ANKRD20A1 ankyrin repeat domain 20 family member A1 441430 ANKRD20A2 ankyrin repeat domain 20 family member A2 441425 ANKRD20A3 ankyrin repeat domain 20 family member A3 728747 ANKRD20A4 ankyrin repeat domain 20 family member A4 170961 ANKRD24 ankyrin repeat domain 24 22852 ANKRD26 ankyrin repeat domain 26 84079 ANKRD27 ankyrin repeat domain 27 91074 ANKRD30A ankyrin repeat domain 30A 374860 ANKRD30B ankyrin repeat domain 30B 148741 ANKRD35 ankyrin repeat domain 35 375248 ANKRD36 ankyrin repeat domain 36 400986 ANKRD36C ankyrin repeat domain 36C 353322 ANKRD37 ankyrin repeat domain 37 57182 ANKRD50 ankyrin repeat domain 50 79722 ANKRD55 ankyrin repeat domain 55 22881 ANKRD6 ankyrin repeat domain 6 342850 ANKRD62 ankyrin repeat domain 62 100131244 ANKRD63 ankyrin repeat domain 63 122416 ANKRD9 ankyrin repeat domain 9 23294 ANKS1A ankyrin repeat and sterile alpha motif domain containing 1A 124401 ANKS3 ankyrin repeat and sterile alpha motif domain containing 3 257629 ANKS4B ankyrin repeat and sterile alpha motif domain containing 4B 203286 ANKS6 ankyrin repeat and sterile alpha motif domain containing 6 142685 ASB15 ankyrin repeat and SOCS box containing 15 92591 ASB16 ankyrin repeat and SOCS box containing 16 401036 ASB18 ankyrin repeat and SOCS box containing 18 51676 ASB2 ankyrin repeat and SOCS box containing 2 140459 ASB6 ankyrin repeat and SOCS box containing 6 136991 ASZ1 ankyrin repeat, SAM and basic leucine zipper domain containing 1 57513 CASKIN2 CASK interacting protein 2 83715 ESPN espin 339768 ESPNL espin like 10116 FEM1B fem-1 homolog B 100526835 FPGT-TNNI3K FPGT-TNNI3K readthrough 2553 GABPB2 GA binding protein transcription factor subunit beta 1 27130 INVS inversin 57498 KIDINS220 kinase D interacting substrate 220 64332 NFKBIZ NFKB inhibitor zeta 284353 NKPD1 NTPase KAP family P-loop domain containing 1 100287399 POTEB POTE ankyrin domain family member B2 388468 POTEC POTE ankyrin domain family member C 317754 POTED POTE ankyrin domain family member D 404785 POTEG POTE ankyrin domain family member G 23784 POTEH POTE ankyrin domain family member H 641455 POTEM POTE ankyrin domain family member M 26064 RAI14 retinoic acid induced 14 65124 SOWAHC sosondowah ankyrin repeat domain family member C 26115 TANC2 tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 2 51086 TNNI3K TNNI3 interacting kinase 4796 TONSL tonsoku like, DNA repair protein 55075 UACA uveal autoantigen with coiled-coil domains and ankyrin repeats 124590 USH1G USH1 protein network component sans

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 1.86e-03 1.98e-04 GO retrograde transport, endosome to plasma membrane 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 1.49e-04 2.92e-02 ubiquitin protein ligase binding 1.61e-04 3.13e-02 ubiquitin-like protein ligase binding 2.03e-04 3.64e-02 filamentous actin 3.39e-04 5.76e-02 ubiquitin ligase complex 5.99e-04 9.85e-02 ubiquitin-protein transferase activity 6.42e-04 1.37e-01 regulation of canonical Wnt signaling pathway 7.37e-04 1.18e-01 ubiquitin-like protein transferase activity 8.14e-04 1.67e-01 retrograde transport, endosome to plasma membrane 1.29e-03 2.43e-01 regulation of heart rate 1.46e-03 2.69e-01 regulation of Wnt signaling pathway 1.48e-03 2.72e-01 protein ubiquitination 2.11e-03 3.56e-01 protein modification by small protein conjugation 2.13e-03 3.58e-01 regulation of cardiac conduction 2.36e-03 3.89e-01 actin filament bundle organization 2.36e-03 3.89e-01 actin filament bundle assembly 3.59e-03 4.25e-01 actin filament 3.70e-03 5.59e-01 positive regulation of cell projection organization 3.90e-03 5.71e-01 neuron development 3.90e-03 5.71e-01 branching involved in prostate gland morphogenesis 3.90e-03 5.71e-01 epithelial cell maturation involved in prostate gland development

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 5.42e-05 8.99e-03 ANTIGEN PROCESSING UBIQUITINATION PROTEASOME DEGRADATION 8.31e-05 1.31e-02 CLASS I MHC MEDIATED ANTIGEN PROCESSING PRESENTATION 5.60e-04 5.99e-02 ANTIGEN PROCESSING UBIQUITINATION PROTEASOME DEGRADATION 6.42e-04 6.76e-02 CLASS I MHC MEDIATED ANTIGEN PROCESSING PRESENTATION 1.72e-03 1.87e-01 PROLONGED ERK ACTIVATION EVENTS 1.72e-03 1.87e-01 ARMS MEDIATED ACTIVATION 1.81e-03 1.71e-01 PROLONGED ERK ACTIVATION EVENTS 1.81e-03 1.71e-01 ARMS MEDIATED ACTIVATION 5.16e-03 4.69e-01 SIGNALLING TO ERKS 7.26e-03 5.63e-01 SIGNALLING TO ERKS 1.04e-02 8.21e-01 NGF SIGNALLING VIA TRKA FROM THE PLASMA MEMBRANE 2.04e-02 1.00e+00 NGF SIGNALLING VIA TRKA FROM THE PLASMA MEMBRANE 4.08e-02 1.00e+00 SIGNALLING BY NGF 4.84e-02 1.00e+00 RESPONSE TO ELEVATED PLATELET CYTOSOLIC CA2

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 1.14e-04 2.46e-01 absent cochlear microphonics 2.06e-04 3.55e-01 abnormal utricular macula morphology 3.27e-04 4.72e-01 vestibular saccular macula degeneration 4.29e-04 5.54e-01 vestibular hair cell degeneration 4.83e-04 5.96e-01 reduced linear vestibular evoked potential 6.06e-04 6.78e-01 abnormal inner hair cell stereociliary bundle morphology 9.52e-04 8.78e-01 absent linear vestibular evoked potential 1.55e-03 1.00e+00 bidirectional circling 1.56e-03 1.00e+00 head shaking 2.71e-03 1.00e+00 abnormal reflex 3.51e-03 1.00e+00 dextrocardia 5.61e-03 1.00e+00 abnormal DNA methylation during gametogenesis 5.61e-03 1.00e+00 abnormal conjunctiva goblet cell morphology 5.61e-03 1.00e+00 eyelid edema 5.63e-03 1.00e+00 thin cochlear hair cell stereocilia 6.55e-03 1.00e+00 increased kidney weight 9.35e-03 1.00e+00 abnormal embryonic cilium location or orientation 9.37e-03 1.00e+00 abnormal biliary tract morphology 9.37e-03 1.00e+00 decreased cochlear hair cell stereocilia number 1.02e-02 1.00e+00 impaired swimming

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

²FDR corrected p-value (Benjamini-Hochberg)