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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod43

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod43 Module size 44 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 8447 DOC2B double C2 domain beta 26130 GAPVD1 GTPase activating protein and VPS9 domains 1 11020 IFT27 intraflagellar transport 27 79083 MLPH melanophilin 64284 RAB17 RAB17, member RAS oncogene family 22931 RAB18 RAB18, member RAS oncogene family 55647 RAB20 RAB20, member RAS oncogene family 23011 RAB21 RAB21, member RAS oncogene family 57403 RAB22A RAB22A, member RAS oncogene family 51715 RAB23 RAB23, member RAS oncogene family 53917 RAB24 RAB24, member RAS oncogene family 25837 RAB26 RAB26, member RAS oncogene family 5873 RAB27A RAB27A, member RAS oncogene family 5874 RAB27B RAB27B, member RAS oncogene family 9364 RAB28 RAB28, member RAS oncogene family 27314 RAB30 RAB30, member RAS oncogene family 11031 RAB31 RAB31, member RAS oncogene family 10981 RAB32 RAB32, member RAS oncogene family 83452 RAB33B RAB33B, member RAS oncogene family 83871 RAB34 RAB34, member RAS oncogene family 11021 RAB35 RAB35, member RAS oncogene family 9609 RAB36 RAB36, member RAS oncogene family 326624 RAB37 RAB37, member RAS oncogene family 23682 RAB38 RAB38, member RAS oncogene family 54734 RAB39A RAB39A, member RAS oncogene family 116442 RAB39B RAB39B, member RAS oncogene family 5864 RAB3A RAB3A, member RAS oncogene family 5865 RAB3B RAB3B, member RAS oncogene family 115827 RAB3C RAB3C, member RAS oncogene family 9545 RAB3D RAB3D, member RAS oncogene family 5867 RAB4A RAB4A, member RAS oncogene family 53916 RAB4B RAB4B, member RAS oncogene family 5868 RAB5A RAB5A, member RAS oncogene family 5869 RAB5B RAB5B, member RAS oncogene family 5878 RAB5C RAB5C, member RAS oncogene family 8934 RAB7L1 RAB29, member RAS oncogene family 9367 RAB9A RAB9A, member RAS oncogene family 9135 RABEP1 rabaptin, RAB GTPase binding effector protein 1 5877 RABIF RAB interacting factor 168433 RNF133 ring finger protein 133 378925 RNF148 ring finger protein 148 22895 RPH3A rabphilin 3A 9501 RPH3AL rabphilin 3A like (without C2 domains) 23546 SYNGR4 synaptogyrin 4

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 1.97e-01 2.39e-74 GO Rab protein signal transduction biological_process 1.87e-01 6.28e-70 Reactome RAB geranylgeranylation Metabolism of proteins 1.68e-01 3.68e-17 GO anchored component of synaptic vesicle membrane cellular_component 7.63e-02 3.00e-16 GO GTP-dependent protein binding molecular_function 6.84e-03 1.97e-12 GO regulation of endocytosis biological_process 1.50e-03 1.96e-16 GO antigen processing and presentation 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 0.00e+00 0.00e+00 small GTPase mediated signal transduction 0.00e+00 0.00e+00 regulation of vesicle-mediated transport 0.00e+00 0.00e+00 regulation of secretion 0.00e+00 0.00e+00 regulation of exocytosis 0.00e+00 0.00e+00 cytoplasmic vesicle membrane 0.00e+00 0.00e+00 vesicle membrane 0.00e+00 0.00e+00 endosome 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 myosin V binding 0.00e+00 0.00e+00 GTPase activity 0.00e+00 0.00e+00 GDP binding 0.00e+00 0.00e+00 nucleoside-triphosphatase activity 0.00e+00 0.00e+00 GTP-dependent protein binding 2.38e-10 1.90e-07 positive regulation of exocytosis 1.17e-09 8.63e-07 exocytosis 1.73e-09 1.25e-06 regulation of endocytosis

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 9.01e-03 6.75e-01 DOPAMINE NEUROTRANSMITTER RELEASE CYCLE 9.77e-03 7.87e-01 ACETYLCHOLINE NEUROTRANSMITTER RELEASE CYCLE 1.08e-02 7.78e-01 NOREPINEPHRINE NEUROTRANSMITTER RELEASE CYCLE 1.08e-02 7.78e-01 ACETYLCHOLINE NEUROTRANSMITTER RELEASE CYCLE 1.26e-02 8.86e-01 GABA SYNTHESIS RELEASE REUPTAKE AND DEGRADATION 1.27e-02 9.62e-01 DOPAMINE NEUROTRANSMITTER RELEASE CYCLE 1.29e-02 9.02e-01 INSULIN SYNTHESIS AND PROCESSING 1.37e-02 1.00e+00 NOREPINEPHRINE NEUROTRANSMITTER RELEASE CYCLE 1.49e-02 1.00e+00 GLUTAMATE NEUROTRANSMITTER RELEASE CYCLE 1.62e-02 1.00e+00 GLUTAMATE NEUROTRANSMITTER RELEASE CYCLE 1.81e-02 1.00e+00 INSULIN SYNTHESIS AND PROCESSING 2.16e-02 1.00e+00 GABA SYNTHESIS RELEASE REUPTAKE AND DEGRADATION 2.86e-02 1.00e+00 NEUROTRANSMITTER RELEASE CYCLE 3.64e-02 1.00e+00 NEUROTRANSMITTER RELEASE CYCLE 3.75e-02 1.00e+00 GOLGI ASSOCIATED VESICLE BIOGENESIS 4.51e-02 1.00e+00 TRANS GOLGI NETWORK VESICLE BUDDING

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 7.71e-05 1.91e-01 diluted coat color 2.42e-04 3.94e-01 abnormal platelet dense granule physiology 3.01e-04 4.47e-01 abnormal skin pigmentation 4.23e-04 5.51e-01 decreased platelet serotonin level 5.80e-04 6.63e-01 abnormal platelet dense granule number 1.87e-03 1.00e+00 increased circulating fructosamine level 3.74e-03 1.00e+00 abnormal spinal cord central canal morphology 3.74e-03 1.00e+00 dilated pulmonary alveolar ducts 3.74e-03 1.00e+00 abnormal hair follicle melanogenesis 3.74e-03 1.00e+00 abnormal lung position or orientation 4.61e-03 1.00e+00 decreased platelet aggregation 5.52e-03 1.00e+00 abnormal coat/hair pigmentation 5.61e-03 1.00e+00 increased circulating lactate dehydrogenase level 5.61e-03 1.00e+00 decreased NK cell degranulation 5.61e-03 1.00e+00 abnormal neural tube ventricular layer morphology 5.61e-03 1.00e+00 abnormal pupillary reflex 5.61e-03 1.00e+00 misaligned sternebrae 5.61e-03 1.00e+00 lung cysts 7.47e-03 1.00e+00 abnormal Harderian gland pigmentation 7.47e-03 1.00e+00 abnormal melanocyte morphology

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

²FDR corrected p-value (Benjamini-Hochberg)