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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod42

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod42 Module size 48 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 10282 BET1 Bet1 golgi vesicular membrane trafficking protein 51272 BET1L Bet1 golgi vesicular membrane trafficking protein like 662 BNIP1 BCL2 interacting protein 1 10814 CPLX2 complexin 2 9527 GOSR1 golgi SNAP receptor complex member 1 9570 GOSR2 golgi SNAP receptor complex member 2 9476 NAPA napsin A aspartic peptidase 256236 NAPB napsin B aspartic peptidase, pseudogene 8774 NAPG NSF attachment protein gamma 192683 SCAMP5 secretory carrier membrane protein 5 23256 SCFD1 sec1 family domain containing 1 26984 SEC22A SEC22 homolog A, vesicle trafficking protein 9117 SEC22C SEC22 homolog C, vesicle trafficking protein 8773 SNAP23 synaptosome associated protein 23 9342 SNAP29 synaptosome associated protein 29 116841 SNAP47 synaptosome associated protein 47 8677 STX10 syntaxin 10 8676 STX11 syntaxin 11 23673 STX12 syntaxin 12 8675 STX16 syntaxin 16 100534593 STX16-NPEPL1 STX16-NPEPL1 readthrough (NMD candidate) 55014 STX17 syntaxin 17 53407 STX18 syntaxin 18 415117 STX19 syntaxin 19 6804 STX1A syntaxin 1A 112755 STX1B syntaxin 1B 2054 STX2 syntaxin 2 6809 STX3 syntaxin 3 6810 STX4 syntaxin 4 6811 STX5 syntaxin 5 10228 STX6 syntaxin 6 8417 STX7 syntaxin 7 9482 STX8 syntaxin 8 6812 STXBP1 syntaxin binding protein 1 9515 STXBP5L syntaxin binding protein 5 like 203062 TSNARE1 t-SNARE domain containing 1 65264 USE1 ubiquitin conjugating enzyme E2 Z 6843 VAMP1 vesicle associated membrane protein 1 6844 VAMP2 vesicle associated membrane protein 2 9341 VAMP3 vesicle associated membrane protein 3 8674 VAMP4 vesicle associated membrane protein 4 10791 VAMP5 vesicle associated membrane protein 5 6845 VAMP7 vesicle associated membrane protein 7 8673 VAMP8 vesicle associated membrane protein 8 11311 VPS45 vacuolar protein sorting 45 homolog 143187 VTI1A vesicle transport through interaction with t-SNAREs 1A 10490 VTI1B vesicle transport through interaction with t-SNAREs 1B 10652 YKT6 YKT6 v-SNARE homolog

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 3.92e-01 5.08e-96 GO SNARE complex cellular_component 3.13e-01 7.95e-76 GO SNAP receptor activity molecular_function 9.95e-02 1.81e-20 GO presynaptic active zone membrane cellular_component 5.17e-02 1.23e-52 GO vesicle fusion biological_process 3.45e-02 2.65e-14 GO vesicle docking involved in exocytosis biological_process 2.97e-02 5.22e-24 Reactome Intra-Golgi traffic Vesicle-mediated transport 2.44e-02 1.14e-04 Reactome Toxicity of botulinum toxin type F (BoNT/F) Disease 2.43e-02 1.14e-04 Reactome Toxicity of botulinum toxin type D (BoNT/D) Disease 1.90e-02 4.53e-19 GO membrane fusion biological_process 1.56e-02 1.29e-08 GO Golgi to plasma membrane protein transport biological_process 1.43e-02 3.23e-17 Reactome COPII-mediated vesicle transport Metabolism of proteins#Vesicle-mediated transport 1.08e-02 1.54e-40 GO vesicle docking biological_process 6.94e-03 2.01e-31 GO syntaxin binding molecular_function 3.39e-03 4.57e-05 Reactome Toxicity of botulinum toxin type G (BoNT/G) Disease

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 membrane docking 0e+00 0e+00 plasma membrane fusion 0e+00 0e+00 exocytosis 0e+00 0e+00 neurotransmitter transport 0e+00 0e+00 organelle localization 0e+00 0e+00 organelle fusion 0e+00 0e+00 synaptic vesicle transport 0e+00 0e+00 vesicle organization 0e+00 0e+00 regulation of neurotransmitter levels 0e+00 0e+00 vesicle localization 0e+00 0e+00 synaptic vesicle exocytosis 0e+00 0e+00 membrane fusion 0e+00 0e+00 neurotransmitter secretion 0e+00 0e+00 vesicle fusion 0e+00 0e+00 establishment of vesicle localization 0e+00 0e+00 vesicle docking 0e+00 0e+00 synaptic vesicle fusion to presynaptic active zone membrane 0e+00 0e+00 calcium ion regulated exocytosis 0e+00 0e+00 establishment of organelle localization 0e+00 0e+00 regulation of vesicle-mediated transport

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 PROTEOLYTIC CLEAVAGE OF SNARE COMPLEX PROTEINS 0.00e+00 0.00e+00 NEURONAL SYSTEM 0.00e+00 0.00e+00 BOTULINUM NEUROTOXICITY 0.00e+00 0.00e+00 PROTEOLYTIC CLEAVAGE OF SNARE COMPLEX PROTEINS 0.00e+00 0.00e+00 NEURONAL SYSTEM 0.00e+00 0.00e+00 BOTULINUM NEUROTOXICITY 2.80e-07 6.83e-05 TRANS GOLGI NETWORK VESICLE BUDDING 1.53e-06 3.35e-04 NOREPINEPHRINE NEUROTRANSMITTER RELEASE CYCLE 2.67e-06 4.34e-04 TRANS GOLGI NETWORK VESICLE BUDDING 2.96e-06 6.15e-04 ACETYLCHOLINE NEUROTRANSMITTER RELEASE CYCLE 3.55e-06 5.68e-04 NOREPINEPHRINE NEUROTRANSMITTER RELEASE CYCLE 4.55e-06 7.21e-04 DOPAMINE NEUROTRANSMITTER RELEASE CYCLE 4.70e-06 7.43e-04 ACETYLCHOLINE NEUROTRANSMITTER RELEASE CYCLE 5.57e-06 1.11e-03 MEMBRANE TRAFFICKING 8.02e-06 1.56e-03 GLUTAMATE NEUROTRANSMITTER RELEASE CYCLE 1.16e-05 1.71e-03 GLUTAMATE NEUROTRANSMITTER RELEASE CYCLE 1.20e-05 2.26e-03 DOPAMINE NEUROTRANSMITTER RELEASE CYCLE 1.62e-05 2.98e-03 GABA SYNTHESIS RELEASE REUPTAKE AND DEGRADATION 2.46e-05 3.46e-03 GABA SYNTHESIS RELEASE REUPTAKE AND DEGRADATION 4.98e-05 6.68e-03 MEMBRANE TRAFFICKING

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 1.60e-04 3.08e-01 abnormal adrenal chromaffin cell morphology 6.87e-04 7.28e-01 abnormal neuron physiology 1.54e-03 1.00e+00 abnormal synaptic vesicle recycling 1.87e-03 1.00e+00 decreased susceptibility to induced pancreatitis 3.03e-03 1.00e+00 decreased body temperature 3.54e-03 1.00e+00 abnormal synaptic vesicle number 7.48e-03 1.00e+00 decreased NK cell degranulation 7.48e-03 1.00e+00 enlarged gallbladder 7.48e-03 1.00e+00 liver cysts 9.03e-03 1.00e+00 abnormal platelet physiology 9.34e-03 1.00e+00 colorless urine 9.34e-03 1.00e+00 tail dragging 9.34e-03 1.00e+00 abnormal brain ventricular system morphology 9.34e-03 1.00e+00 abnormal cortical marginal zone morphology 9.35e-03 1.00e+00 abnormal third ventricle morphology 1.12e-02 1.00e+00 abnormal hypothalamus secretion 1.12e-02 1.00e+00 novel environmental response-related retropulsion 1.12e-02 1.00e+00 abnormal brain ependyma morphology 1.17e-02 1.00e+00 impaired righting response 1.17e-02 1.00e+00 abnormal posture

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

²FDR corrected p-value (Benjamini-Hochberg)