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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod317

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod317 Module size 40 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 1122 CHML CHM like, Rab escort protein 2 51277 DNAJC27 DnaJ heat shock protein family (Hsp40) member C27 407738 FAM19A1 family with sequence similarity 19 member A1, C-C motif chemokine like 2664 GDI1 GDP dissociation inhibitor 1 84953 MICALCL MICAL C-terminal like 8766 RAB11A RAB11A, member RAS oncogene family 9230 RAB11B RAB11B, member RAS oncogene family 201475 RAB12 RAB12, member RAS oncogene family 376267 RAB15 RAB15, member RAS oncogene family 401409 RAB19 RAB19, member RAS oncogene family 5861 RAB1A RAB1A, member RAS oncogene family 81876 RAB1B RAB1B, member RAS oncogene family 57111 RAB25 RAB25, member RAS oncogene family 5862 RAB2A RAB2A, member RAS oncogene family 84932 RAB2B RAB2B, member RAS oncogene family 9363 RAB33A RAB33A, member RAS oncogene family 142684 RAB40A RAB40A, member RAS oncogene family 282808 RAB40AL RAB40A like 10966 RAB40B RAB40B, member RAS oncogene family 57799 RAB40C RAB40C, member RAS oncogene family 347517 RAB41 RAB41, member RAS oncogene family 339122 RAB43 RAB43, member RAS oncogene family 5870 RAB6A RAB6A, member RAS oncogene family 51560 RAB6B RAB6B, member RAS oncogene family 84084 RAB6C RAB6C, member RAS oncogene family 7879 RAB7A RAB7A, member RAS oncogene family 51762 RAB8B RAB8B, member RAS oncogene family 51209 RAB9B RAB9B, member RAS oncogene family 10567 RABAC1 Rab acceptor 1 5876 RABGGTB Rab geranylgeranyltransferase subunit beta 11158 RABL2B RAB, member of RAS oncogene family like 2B 55684 RABL6 RAB, member RAS oncogene family like 6 128637 TBC1D20 TBC1 domain family member 20 25771 TBC1D22A TBC1 domain family member 22A 55633 TBC1D22B TBC1 domain family member 22B 10897 YIF1A Yip1 interacting factor homolog A, membrane trafficking protein 90522 YIF1B Yip1 interacting factor homolog B, membrane trafficking protein 81555 YIPF5 Yip1 domain family member 5 286451 YIPF6 Yip1 domain family member 6 285525 YIPF7 Yip1 domain family member 7

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 2.07e-01 7.35e-56 GO Rab protein signal transduction biological_process 1.16e-01 5.95e-09 GO virion assembly biological_process 8.29e-02 1.39e-48 Reactome RAB geranylgeranylation Metabolism of proteins 5.92e-02 6.74e-05 GO protein geranylgeranylation biological_process 1.42e-02 1.74e-06 GO COPII-coated ER to Golgi transport vesicle cellular_component 7.14e-03 9.62e-15 Reactome TBC/RABGAPs Vesicle-mediated transport

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 small GTPase mediated signal transduction 0.00e+00 0.00e+00 transport vesicle 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 nucleoside binding 0.00e+00 0.00e+00 GTPase activity 3.88e-10 3.03e-07 protein secretion 6.32e-10 3.45e-07 GDP binding 9.83e-10 7.34e-07 peptide secretion 1.33e-09 9.74e-07 vesicle docking involved in exocytosis 2.07e-09 1.48e-06 Golgi vesicle transport 2.73e-09 1.92e-06 endosomal transport 3.07e-09 2.15e-06 membrane docking 5.44e-09 2.58e-06 myosin V binding 1.06e-08 6.87e-06 vesicle docking 1.16e-08 4.56e-06 Golgi membrane 2.27e-08 1.41e-05 regulation of vesicle-mediated transport 4.22e-08 2.52e-05 retrograde transport, endosome to Golgi

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 1.28e-02 8.97e-01 REGULATION OF WATER BALANCE BY RENAL AQUAPORINS 1.29e-02 9.73e-01 REGULATION OF WATER BALANCE BY RENAL AQUAPORINS 1.50e-02 1.00e+00 PRE NOTCH PROCESSING IN GOLGI 1.93e-02 1.00e+00 PRE NOTCH EXPRESSION AND PROCESSING 1.93e-02 1.00e+00 AQUAPORIN MEDIATED TRANSPORT 2.23e-02 1.00e+00 PRE NOTCH PROCESSING IN GOLGI 2.83e-02 1.00e+00 AQUAPORIN MEDIATED TRANSPORT 4.60e-02 1.00e+00 PRE NOTCH EXPRESSION AND PROCESSING 4.93e-02 1.00e+00 ACTIVATION OF CHAPERONE GENES BY XBP1S

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 shiny fur 3.74e-03 1e+00 decreased Paneth cell number 3.74e-03 1e+00 abnormal Golgi apparatus morphology 3.74e-03 1e+00 decreased synaptic glutamate release 3.75e-03 1e+00 abnormal hippocampus CA3 region morphology 5.61e-03 1e+00 esophageal atresia 5.61e-03 1e+00 decreased aggression towards mice 5.61e-03 1e+00 abnormal synaptic glutamate release 7.46e-03 1e+00 esophageal epithelium hyperplasia 7.47e-03 1e+00 abnormal vagina epithelium morphology 7.47e-03 1e+00 ruptured lens capsule 7.47e-03 1e+00 absent acrosome 9.33e-03 1e+00 abnormal Paneth cell morphology 9.33e-03 1e+00 abnormal primitive streak elongation 9.36e-03 1e+00 colitis 1.31e-02 1e+00 abnormal seminiferous tubule epithelium morphology 1.49e-02 1e+00 abnormal pancreatic acinar cell morphology 1.68e-02 1e+00 increased susceptibility to weight loss 1.68e-02 1e+00 abnormal hippocampal mossy fiber morphology 1.86e-02 1e+00 abnormal intestinal goblet cell morphology

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

²FDR corrected p-value (Benjamini-Hochberg)