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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod208

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod208 Module size 62 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 3267 AGFG1 ArfGAP with FG repeats 1 306 ANXA3 annexin A3 8943 AP3D1 adaptor related protein complex 3 subunit delta 1 55130 ARMC4 armadillo repeat containing 4 439 ASNA1 arsA arsenite transporter, ATP-binding, homolog 1 (bacterial) 168090 C6orf118 chromosome 6 open reading frame 118 643677 CCDC168 coiled-coil domain containing 168 1113 CHGA chromogranin A 1114 CHGB chromogranin B 10175 CNIH cornichon family AMPA receptor auxiliary protein 1 29097 CNIH4 cornichon family AMPA receptor auxiliary protein 4 9382 COG1 component of oligomeric golgi complex 1 314030 COG2 component of oligomeric golgi complex 5 83548 COG3 component of oligomeric golgi complex 3 361407 COG4 component of oligomeric golgi complex 4 293456 COG5 component of oligomeric golgi complex 7 310411 COG6 component of oligomeric golgi complex 6 293456 COG7 component of oligomeric golgi complex 7 84342 COG8 component of oligomeric golgi complex 8 23317 DNAJC13 DnaJ heat shock protein family (Hsp40) member C13 10938 EHD1 EH domain containing 1 30845 EHD3 EH domain containing 3 79632 FAM184A family with sequence similarity 184 member A 92002 FAM58A cyclin Q 153643 FAM81B family with sequence similarity 81 member B 2802 GOLGA3 golgin A3 9950 GOLGA5 golgin A5 127845 GOLT1A golgi transport 1A 51026 GOLT1B golgi transport 1B 79772 MCTP1 multiple C2 and transmembrane domain containing 1 84315 MON1A MON1 homolog A, secretory trafficking associated 22879 MON1B MON1 homolog B, secretory trafficking associated 4905 NSF N-ethylmaleimide sensitive factor, vesicle fusing ATPase 4976 OPA1 OPA1, mitochondrial dynamin like GTPase 138428 PTRH1 peptidyl-tRNA hydrolase 1 homolog 60561 RINT1 RAD50 interactor 1 27156 RTDR1 radial spoke head 14 homolog 113402 SFT2D1 SFT2 domain containing 1 375035 SFT2D2 SFT2 domain containing 2 84826 SFT2D3 SFT2 domain containing 3 6813 STXBP2 syntaxin binding protein 2 252983 STXBP4 syntaxin binding protein 4 51430 SUCO SUN domain containing ossification factor 202018 TAPT1 transmembrane anterior posterior transformation 1 9392 TGFBRAP1 transforming growth factor beta receptor associated protein 1 8615 USO1 USO1 vesicle transport factor 7405 UVRAG UV radiation resistance associated 63894 VIPAS39 VPS33B interacting protein, apical-basolateral polarity regulator, spe-39 homolog 64601 VPS16 VPS16, CORVET/HOPS core subunit 57617 VPS18 VPS18, CORVET/HOPS core subunit 65082 VPS33A VPS33A, CORVET/HOPS core subunit 26276 VPS33B VPS33B, late endosome and lysosome associated 23339 VPS39 VPS39, HOPS complex subunit 27072 VPS41 VPS41, HOPS complex subunit 738 VPS51 VPS51, GARP complex subunit 6293 VPS52 VPS52, GARP complex subunit 55275 VPS53 VPS53, GARP complex subunit 51542 VPS54 VPS54, GARP complex subunit 23355 VPS8 VPS8, CORVET complex subunit 7485 WRB tryptophan rich basic protein 84287 ZDHHC16 zinc finger DHHC-type containing 16 64145 ZFYVE20 rabenosyn, RAB effector

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 4.74e-01 2.92e-10 GO GARP complex cellular_component 4.53e-01 4.07e-21 GO Golgi transport complex cellular_component 3.15e-01 7.13e-18 GO HOPS complex cellular_component 2.57e-01 8.17e-14 GO AP-3 adaptor complex cellular_component 1.11e-01 1.19e-04 GO tail-anchored membrane protein insertion into ER membrane biological_process 5.74e-02 3.55e-23 Reactome Retrograde transport at the Trans-Golgi-Network Vesicle-mediated transport 3.93e-02 3.09e-17 Reactome Intra-Golgi traffic Vesicle-mediated transport 1.69e-02 1.43e-08 GO endocytic recycling biological_process 7.13e-03 6.10e-04 GO specific granule cellular_component

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 ER to Golgi vesicle-mediated transport 0.00e+00 0.00e+00 intra-Golgi vesicle-mediated transport 0.00e+00 0.00e+00 Golgi vesicle transport 0.00e+00 0.00e+00 endomembrane system organization 0.00e+00 0.00e+00 vacuolar transport 0.00e+00 0.00e+00 endosomal transport 0.00e+00 0.00e+00 lysosomal transport 0.00e+00 0.00e+00 endosome to lysosome transport 0.00e+00 0.00e+00 organelle fusion 0.00e+00 0.00e+00 Golgi transport complex 0.00e+00 0.00e+00 trans-Golgi network membrane 0.00e+00 0.00e+00 HOPS complex 9.41e-11 4.87e-08 AP-3 adaptor complex 1.71e-10 8.56e-08 GARP complex 2.39e-10 1.17e-07 Golgi membrane 2.86e-10 2.27e-07 endocytic recycling 4.59e-10 3.55e-07 vesicle organization 1.47e-09 6.48e-07 trans-Golgi network 1.94e-09 1.39e-06 Golgi organization 2.08e-09 1.49e-06 vacuole fusion

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 1.72e-03 1.87e-01 TRAFFICKING OF GLUR2 CONTAINING AMPA RECEPTORS 3.44e-03 3.35e-01 TRAFFICKING OF AMPA RECEPTORS 3.62e-03 3.12e-01 TRAFFICKING OF GLUR2 CONTAINING AMPA RECEPTORS 3.63e-03 3.13e-01 FACTORS INVOLVED IN MEGAKARYOCYTE DEVELOPMENT AND PLATELET PRODUCTION 3.63e-03 3.13e-01 TRAFFICKING OF AMPA RECEPTORS 4.29e-03 4.03e-01 FACTORS INVOLVED IN MEGAKARYOCYTE DEVELOPMENT AND PLATELET PRODUCTION 1.48e-02 1.00e+00 TOLL RECEPTOR CASCADES 1.72e-02 1.00e+00 TOLL RECEPTOR CASCADES 2.92e-02 1.00e+00 NEUROTRANSMITTER RECEPTOR BINDING AND DOWNSTREAM TRANSMISSION IN THE POSTSYNAPTIC CELL 4.21e-02 1.00e+00 TRANSMISSION ACROSS CHEMICAL SYNAPSES 4.68e-02 1.00e+00 NEUROTRANSMITTER RECEPTOR BINDING AND DOWNSTREAM TRANSMISSION IN THE POSTSYNAPTIC CELL

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 1.42e-04 2.87e-01 globozoospermia 1.46e-03 1.00e+00 abnormal adrenaline level 1.46e-03 1.00e+00 abnormal adrenal gland secretion 1.75e-03 1.00e+00 arrest of spermiogenesis 1.89e-03 1.00e+00 complete preweaning lethality 2.97e-03 1.00e+00 complete embryonic lethality 3.54e-03 1.00e+00 abnormal lysosome morphology 3.89e-03 1.00e+00 preweaning lethality 4.46e-03 1.00e+00 abnormal cell morphology 5.08e-03 1.00e+00 abnormal acrosome morphology 5.63e-03 1.00e+00 decreased circulating estrogen level 7.09e-03 1.00e+00 asthenozoospermia 7.51e-03 1.00e+00 abnormal Golgi apparatus morphology 7.88e-03 1.00e+00 abnormal gametogenesis 9.35e-03 1.00e+00 increased mesothelioma incidence 1.12e-02 1.00e+00 enhanced sensorimotor gating 1.12e-02 1.00e+00 abnormal lateral plate mesoderm morphology 1.12e-02 1.00e+00 abnormal GABAergic neuron physiology 1.12e-02 1.00e+00 absent dorsal root ganglion 1.19e-02 1.00e+00 diluted coat color

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

²FDR corrected p-value (Benjamini-Hochberg)