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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod143

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod143 Module size 36 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 79738 BBS10 Bardet-Biedl syndrome 10 10576 CCT2 chaperonin containing TCP1 subunit 2 7203 CCT3 chaperonin containing TCP1 subunit 3 10575 CCT4 chaperonin containing TCP1 subunit 4 22948 CCT5 chaperonin containing TCP1 subunit 5 908 CCT6A chaperonin containing TCP1 subunit 6A 10693 CCT6B chaperonin containing TCP1 subunit 6B 10574 CCT7 chaperonin containing TCP1 subunit 7 10694 CCT8 chaperonin containing TCP1 subunit 8 150160 CCT8L2 chaperonin containing TCP1 subunit 8 like 2 55917 CTTNBP2NL CTTNBP2 N-terminal like 653333 FAM86B2 family with sequence similarity 86 member B2 26127 FGFR1OP2 FGFR1 oncogene partner 2 3336 HSPE1 heat shock protein family E (Hsp10) member 1 92342 METTL18 methyltransferase like 18 25895 METTL21B EEF1A lysine methyltransferase 3 8195 MKKS McKusick-Kaufman syndrome 25843 MOB4 MOB family member 4, phocein 4973 OLR1 oxidized low density lipoprotein receptor 1 135138 PACRG parkin coregulated 11235 PDCD10 programmed cell death 10 132954 PDCL2 phosducin like 2 79031 PDCL3 phosducin like 3 5201 PFDN1 prefoldin subunit 1 80143 SIKE1 suppressor of IKBKE 1 85369 STRIP1 striatin interacting protein 1 57464 STRIP2 striatin interacting protein 2 6801 STRN striatin 29966 STRN3 striatin 3 29888 STRN4 striatin 4 6950 TCP1 t-complex 1 80342 TRAF3IP3 TRAF3 interacting protein 3 118813 ZFYVE27 zinc finger FYVE-type containing 27 11055 ZPBP zona pellucida binding protein 124626 ZPBP2 zona pellucida binding protein 2 54764 ZRANB1 zinc finger RANBP2-type containing 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 4.59e-01 1.66e-27 GO chaperonin-containing T-complex cellular_component 2.37e-01 1.08e-24 Reactome Folding of actin by CCT/TriC Metabolism of proteins 1.38e-01 5.39e-07 GO armadillo repeat domain binding molecular_function 6.05e-02 3.32e-21 GO positive regulation of establishment of protein localization to telomere biological_process 2.35e-02 2.59e-07 GO protein phosphatase 2A binding molecular_function 1.46e-02 3.39e-08 GO chaperone-mediated protein complex assembly biological_process 7.38e-03 1.68e-15 GO binding of sperm to zona pellucida biological_process 6.19e-03 1.25e-21 Reactome Prefoldin mediated transfer of substrate to CCT/TriC Metabolism of proteins

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 positive regulation of telomerase RNA localization to Cajal body 0e+00 0e+00 positive regulation of establishment of protein localization to telomere 0e+00 0e+00 regulation of telomere maintenance via telomere lengthening 0e+00 0e+00 positive regulation of protein localization to Cajal body 0e+00 0e+00 chaperone-mediated protein folding 0e+00 0e+00 positive regulation of telomere maintenance via telomere lengthening 0e+00 0e+00 positive regulation of protein localization to chromosome, telomeric region 0e+00 0e+00 single fertilization 0e+00 0e+00 regulation of establishment of protein localization to chromosome 0e+00 0e+00 positive regulation of DNA biosynthetic process 0e+00 0e+00 positive regulation of telomere maintenance 0e+00 0e+00 regulation of telomere maintenance 0e+00 0e+00 sperm-egg recognition 0e+00 0e+00 cell recognition 0e+00 0e+00 protein folding 0e+00 0e+00 toxin transport 0e+00 0e+00 'de novo' protein folding 0e+00 0e+00 cell-cell recognition 0e+00 0e+00 binding of sperm to zona pellucida 0e+00 0e+00 positive regulation of telomere maintenance via telomerase

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 0.00e+00 0.00e+00 PROTEIN FOLDING 0.00e+00 0.00e+00 PREFOLDIN MEDIATED TRANSFER OF SUBSTRATE TO CCT TRIC 0.00e+00 0.00e+00 ASSOCIATION OF TRIC CCT WITH TARGET PROTEINS DURING BIOSYNTHESIS 0.00e+00 0.00e+00 FORMATION OF TUBULIN FOLDING INTERMEDIATES BY CCT TRIC 0.00e+00 0.00e+00 PROTEIN FOLDING 0.00e+00 0.00e+00 PREFOLDIN MEDIATED TRANSFER OF SUBSTRATE TO CCT TRIC 0.00e+00 0.00e+00 ASSOCIATION OF TRIC CCT WITH TARGET PROTEINS DURING BIOSYNTHESIS 0.00e+00 0.00e+00 FORMATION OF TUBULIN FOLDING INTERMEDIATES BY CCT TRIC 3.30e-03 3.25e-01 TRAF3 DEPENDENT IRF ACTIVATION PATHWAY 3.30e-03 3.25e-01 TRAF6 MEDIATED IRF7 ACTIVATION 1.60e-02 1.00e+00 TRAF3 DEPENDENT IRF ACTIVATION PATHWAY 1.61e-02 1.00e+00 TRAF6 MEDIATED IRF7 ACTIVATION 1.81e-02 1.00e+00 RIG I MDA5 MEDIATED INDUCTION OF IFN ALPHA BETA PATHWAYS 4.78e-02 1.00e+00 RIG I MDA5 MEDIATED INDUCTION OF IFN ALPHA BETA PATHWAYS

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 1.77e-03 1e+00 teratozoospermia 1.87e-03 1e+00 delayed fertilization 3.74e-03 1e+00 abnormal inner hair cell kinocilium morphology 5.61e-03 1e+00 absent acrosome 5.61e-03 1e+00 anosmia 7.47e-03 1e+00 decreased susceptibility to atherosclerosis 7.47e-03 1e+00 sinus inflammation 9.32e-03 1e+00 increased muscle relaxation 9.34e-03 1e+00 decreased aggression 1.12e-02 1e+00 coiled sperm flagellum 1.12e-02 1e+00 altered response of heart to induced stress 1.12e-02 1e+00 abnormal thymus cell ratio 1.30e-02 1e+00 abnormal orientation of outer hair cell stereociliary bundles 1.30e-02 1e+00 myocardial trabeculae hypoplasia 1.30e-02 1e+00 partial embryonic lethality between somite formation and embryo turning 1.30e-02 1e+00 decreased B-2 B cell number 1.30e-02 1e+00 abnormal hair follicle bulge morphology 1.49e-02 1e+00 detached sperm flagellum 1.49e-02 1e+00 enlarged third ventricle 1.49e-02 1e+00 abnormal olfaction

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

²FDR corrected p-value (Benjamini-Hochberg)