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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod120

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod120 Module size 29 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 148362 BROX BRO1 domain and CAAX motif containing 5119 CHMP1A charged multivesicular body protein 1A 57132 CHMP1B charged multivesicular body protein 1B 27243 CHMP2A charged multivesicular body protein 2A 25978 CHMP2B charged multivesicular body protein 2B 51652 CHMP3 charged multivesicular body protein 3 29082 CHMP4A charged multivesicular body protein 4A 51510 CHMP5 charged multivesicular body protein 5 91782 CHMP7 charged multivesicular body protein 7 93343 FAM125A multivesicular body subunit 12A 89853 FAM125B multivesicular body subunit 12B 113263 GLCCI1 glucocorticoid induced 1 9798 IST1 IST1, ESCRT-III associated factor 129531 MITD1 microtubule interacting and trafficking domain containing 1 123606 NIPA1 NIPA magnesium transporter 1 100526767 RNF103-CHMP3 RNF103-CHMP3 readthrough 11267 SNF8 SNF8, ESCRT-II complex subunit 7251 TSG101 tumor susceptibility 101 51271 UBAP1 ubiquitin associated protein 1 159195 USP54 ubiquitin specific peptidase 54 84313 VPS25 vacuolar protein sorting 25 homolog 300052 VPS28 VPS28, ESCRT-I subunit 51028 VPS36 vacuolar protein sorting 36 homolog 137492 VPS37A VPS37A, ESCRT-I subunit 79720 VPS37B VPS37B, ESCRT-I subunit 55048 VPS37C VPS37C, ESCRT-I subunit 27183 VPS4A vacuolar protein sorting 4 homolog A 9525 VPS4B vacuolar protein sorting 4 homolog B 51534 VTA1 vesicle trafficking 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 5.32e-30 GO ESCRT III complex disassembly biological_process 4.22e-01 2.72e-09 GO ESCRT II complex cellular_component 1.81e-01 6.96e-41 GO viral budding via host ESCRT complex biological_process 1.32e-01 7.84e-55 GO multivesicular body assembly biological_process 1.15e-01 1.04e-15 GO ESCRT I complex cellular_component 8.17e-02 3.76e-47 Reactome Endosomal Sorting Complex Required For Transport (ESCRT) Vesicle-mediated transport 5.76e-02 1.96e-12 GO multivesicular body sorting pathway biological_process 3.78e-02 2.84e-21 GO endosome transport via multivesicular body sorting pathway 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 0e+00 0e+00 multivesicular body organization 0e+00 0e+00 organelle assembly 0e+00 0e+00 vesicle organization 0e+00 0e+00 autophagy 0e+00 0e+00 endomembrane system organization 0e+00 0e+00 ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway 0e+00 0e+00 endosome organization 0e+00 0e+00 vacuolar transport 0e+00 0e+00 endosome transport via multivesicular body sorting pathway 0e+00 0e+00 endosomal transport 0e+00 0e+00 macroautophagy 0e+00 0e+00 multivesicular body assembly 0e+00 0e+00 multi-organism membrane organization 0e+00 0e+00 viral budding 0e+00 0e+00 cell separation after cytokinesis 0e+00 0e+00 cell division 0e+00 0e+00 membrane budding 0e+00 0e+00 viral life cycle 0e+00 0e+00 virion assembly 0e+00 0e+00 viral budding via host ESCRT complex

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 ENDOSOMAL SORTING COMPLEX REQUIRED FOR TRANSPORT ESCRT 0.00e+00 0.00e+00 MEMBRANE TRAFFICKING 0.00e+00 0.00e+00 ENDOSOMAL SORTING COMPLEX REQUIRED FOR TRANSPORT ESCRT 0.00e+00 0.00e+00 MEMBRANE TRAFFICKING 9.47e-12 3.65e-09 MEMBRANE BINDING AND TARGETTING OF GAG PROTEINS 5.12e-10 1.29e-07 MEMBRANE BINDING AND TARGETTING OF GAG PROTEINS 4.19e-09 9.52e-07 LATE PHASE OF HIV LIFE CYCLE 3.99e-08 8.20e-06 HIV LIFE CYCLE 7.43e-08 1.95e-05 LATE PHASE OF HIV LIFE CYCLE 1.43e-07 3.63e-05 HIV LIFE CYCLE 3.76e-07 6.92e-05 HIV INFECTION 5.00e-07 1.18e-04 HIV INFECTION

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 1.87e-03 1e+00 decreased mitotic index 1.88e-03 1e+00 cardia bifida 3.74e-03 1e+00 abnormal parietal endoderm morphology 3.74e-03 1e+00 abnormal chorioallantoic fusion 3.75e-03 1e+00 abnormal hippocampus CA1 region morphology 3.75e-03 1e+00 abnormal neural plate morphology 5.62e-03 1e+00 disorganized extraembryonic tissue 9.34e-03 1e+00 abnormal embryonic-extraembryonic boundary morphology 9.34e-03 1e+00 abnormal dorsal-ventral axis patterning 1.12e-02 1e+00 abnormal synapse morphology 1.12e-02 1e+00 abnormal allantois morphology 1.24e-02 1e+00 preweaning lethality 1.28e-02 1e+00 abnormal dendritic spine morphology 1.31e-02 1e+00 failure of primitive streak formation 1.31e-02 1e+00 abnormal gastrulation 1.50e-02 1e+00 abnormal somite development 2.05e-02 1e+00 abnormal visceral endoderm morphology 2.05e-02 1e+00 absent mesoderm 2.60e-02 1e+00 absent inner cell mass proliferation 3.35e-02 1e+00 abnormal neural tube morphology/development

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

²FDR corrected p-value (Benjamini-Hochberg)