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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod211

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod211 Module size 30 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 392509 ARL13A ADP ribosylation factor like GTPase 13A 402 ARL2 ADP ribosylation factor like GTPase 2 7461 CLIP2 CAP-Gly domain containing linker protein 2 28955 DEXI Dexi homolog 5202 PFDN2 prefoldin subunit 2 5203 PFDN4 prefoldin subunit 4 10471 PFDN6 prefoldin subunit 6 100361193 TBCA - 1155 TBCB tubulin folding cofactor B 116653 TBCC cyclase associated actin cytoskeleton regulatory protein 2 6904 TBCD tubulin folding cofactor D 6905 TBCE tubulin folding cofactor E 122664 TPPP2 tubulin polymerization promoting protein family member 2 10376 TUBA1B tubulin alpha 1b 84790 TUBA1C tubulin alpha 1c 7278 TUBA3C tubulin alpha 3c 113457 TUBA3D tubulin alpha 3d 112714 TUBA3E tubulin alpha 3e 51807 TUBA8 tubulin alpha 8 79861 TUBAL3 tubulin alpha like 3 203068 TUBB tubulin beta class I 81027 TUBB1 tubulin beta 1 class VI 7280 TUBB2A tubulin beta 2A class IIa 347733 TUBB2B tubulin beta 2B class IIb 10381 TUBB3 tubulin beta 3 class III 84617 TUBB6 tubulin beta 6 class V 347688 TUBB8 tubulin beta 8 class VIII 51174 TUBD1 tubulin delta 1 51175 TUBE1 tubulin epsilon 1 7411 VBP1 VHL binding protein 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 4.46e-01 2.27e-43 Reactome Post-chaperonin tubulin folding pathway Metabolism of proteins 1.24e-01 1.29e-38 GO microtubule-based process biological_process 7.11e-02 8.24e-36 Reactome Cooperation of Prefoldin and TriC/CCT in actin and tubulin folding Metabolism of proteins 8.99e-03 7.92e-40 Reactome Protein folding 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 0.00e+00 0.00e+00 microtubule-based process 0.00e+00 0.00e+00 supramolecular fiber 0.00e+00 0.00e+00 microtubule 0.00e+00 0.00e+00 purine nucleoside binding 0.00e+00 0.00e+00 GTP binding 0.00e+00 0.00e+00 ribonucleoside binding 0.00e+00 0.00e+00 guanyl ribonucleotide binding 0.00e+00 0.00e+00 GTPase activity 0.00e+00 0.00e+00 nucleoside-triphosphatase activity 0.00e+00 0.00e+00 nucleoside binding 0.00e+00 0.00e+00 structural molecule activity 0.00e+00 0.00e+00 structural constituent of cytoskeleton 2.60e-11 2.28e-08 tubulin complex assembly 4.96e-10 2.32e-07 prefoldin complex 3.41e-09 2.36e-06 post-chaperonin tubulin folding pathway 7.93e-09 5.21e-06 protein folding 1.55e-08 9.85e-06 microtubule cytoskeleton organization 1.59e-08 7.04e-06 chaperone binding 1.43e-06 6.61e-04 cellular protein complex assembly 2.88e-06 1.25e-03 spindle organization

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 0e+00 0e+00 POST CHAPERONIN TUBULIN FOLDING PATHWAY 0e+00 0e+00 PROTEIN FOLDING 0e+00 0e+00 PREFOLDIN MEDIATED TRANSFER OF SUBSTRATE TO CCT TRIC 0e+00 0e+00 FORMATION OF TUBULIN FOLDING INTERMEDIATES BY CCT TRIC 0e+00 0e+00 POST CHAPERONIN TUBULIN FOLDING PATHWAY 0e+00 0e+00 PROTEIN FOLDING 0e+00 0e+00 PREFOLDIN MEDIATED TRANSFER OF SUBSTRATE TO CCT TRIC 0e+00 0e+00 FORMATION OF TUBULIN FOLDING INTERMEDIATES BY CCT TRIC

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 4.87e-05 1.40e-01 abnormal basal ganglion morphology 6.92e-05 1.77e-01 absent corpus callosum 3.14e-03 1.00e+00 respiratory distress 3.74e-03 1.00e+00 abnormal cortical plate morphology 3.74e-03 1.00e+00 abnormal platelet shape 5.61e-03 1.00e+00 dilated brain ventricles 5.61e-03 1.00e+00 abnormal trochlear nerve morphology 5.62e-03 1.00e+00 progressive muscle weakness 5.62e-03 1.00e+00 abnormal cranial nerve morphology 7.47e-03 1.00e+00 absent anterior commissure 7.47e-03 1.00e+00 abnormal brain internal capsule morphology 7.47e-03 1.00e+00 abnormal oculomotor nerve morphology 7.49e-03 1.00e+00 abnormal brain commissure morphology 7.49e-03 1.00e+00 abnormal trigeminal nerve morphology 9.34e-03 1.00e+00 abnormal anterior commissure morphology 9.35e-03 1.00e+00 motor neuron degeneration 1.12e-02 1.00e+00 decreased midbrain size 1.28e-02 1.00e+00 abnormal choroid plexus morphology 1.31e-02 1.00e+00 abnormal facial nerve morphology 1.67e-02 1.00e+00 abnormal phrenic nerve morphology

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

²FDR corrected p-value (Benjamini-Hochberg)