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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod60

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod60 Module size 50 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 9744 ACAP1 ArfGAP with coiled-coil, ankyrin repeat and PH domains 1 23527 ACAP2 ArfGAP with coiled-coil, ankyrin repeat and PH domains 2 116983 ACAP3 ArfGAP with coiled-coil, ankyrin repeat and PH domains 3 11033 ADAP1 ArfGAP with dual PH domains 1 55803 ADAP2 ArfGAP with dual PH domains 2 375 ARF1 ADP ribosylation factor 1 377 ARF3 ADP ribosylation factor 3 378 ARF4 ADP ribosylation factor 4 381 ARF5 ADP ribosylation factor 5 382 ARF6 ADP ribosylation factor 6 26286 ARFGAP1 ADP ribosylation factor GTPase activating protein 3 84364 ARFGAP2 ADP ribosylation factor GTPase activating protein 2 26286 ARFGAP3 ADP ribosylation factor GTPase activating protein 3 10565 ARFGEF1 ADP ribosylation factor guanine nucleotide exchange factor 1 10564 ARFGEF2 ADP ribosylation factor guanine nucleotide exchange factor 2 400 ARL1 ADP ribosylation factor like GTPase 1 115761 ARL11 ADP ribosylation factor like GTPase 11 80117 ARL14 ADP ribosylation factor like GTPase 14 54622 ARL15 ADP ribosylation factor like GTPase 15 51326 ARL17A ADP ribosylation factor like GTPase 17A 100506084 ARL17B ADP ribosylation factor like GTPase 17B 10124 ARL4A ADP ribosylation factor like GTPase 4A 10123 ARL4C ADP ribosylation factor like GTPase 4C 379 ARL4D ADP ribosylation factor like GTPase 4D 26225 ARL5A ADP ribosylation factor like GTPase 5A 221079 ARL5B ADP ribosylation factor like GTPase 5B 390790 ARL5C ADP ribosylation factor like GTPase 5C 379 ARL6 ADP ribosylation factor like GTPase 4D 132946 ARL9 ADP ribosylation factor like GTPase 9 8853 ASAP2 ArfGAP with SH3 domain, ankyrin repeat and PH domain 2 55616 ASAP3 ArfGAP with SH3 domain, ankyrin repeat and PH domain 3 26958 COPG2 coatomer protein complex subunit gamma 2 9267 CYTH1 cytohesin 1 9266 CYTH2 cytohesin 2 9265 CYTH3 cytohesin 3 27128 CYTH4 cytohesin 4 26269 FBXO8 F-box protein 8 80142 GBF1 prostaglandin E synthase 2 9922 IQSEC1 IQ motif and Sec7 domain 1 23096 IQSEC2 IQ motif and Sec7 domain 2 440073 IQSEC3 IQ motif and Sec7 domain 3 10945 KDELR1 KDEL endoplasmic reticulum protein retention receptor 1 11014 KDELR2 KDEL endoplasmic reticulum protein retention receptor 2 11015 KDELR3 KDEL endoplasmic reticulum protein retention receptor 3 84249 PSD2 pleckstrin and Sec7 domain containing 2 23362 PSD3 pleckstrin and Sec7 domain containing 3 23550 PSD4 pleckstrin and Sec7 domain containing 4 60682 SMAP1 small ArfGAP 1 10902 SMAP2 bromodomain containing 8 25972 UNC50 unc-50 inner nuclear membrane RNA binding protein

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 3.93e-01 7.31e-35 GO regulation of ARF protein signal transduction biological_process 2.52e-01 3.10e-36 GO ARF guanyl-nucleotide exchange factor activity molecular_function 1.21e-01 1.49e-06 GO protein retention in ER lumen biological_process 8.30e-02 1.01e-31 GO vesicle-mediated transport biological_process 4.13e-02 2.41e-18 Reactome COPI-mediated anterograde transport Metabolism of proteins#Vesicle-mediated transport 3.55e-02 2.41e-18 Reactome COPI-dependent Golgi-to-ER retrograde traffic Vesicle-mediated transport 2.08e-02 4.51e-09 GO Golgi to plasma membrane transport biological_process 6.86e-03 2.25e-16 GO retrograde vesicle-mediated transport, Golgi to ER 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 regulation of small GTPase mediated signal transduction 0.00e+00 0.00e+00 regulation of GTPase activity 0.00e+00 0.00e+00 regulation of Ras protein signal transduction 0.00e+00 0.00e+00 regulation of ARF protein signal transduction 0.00e+00 0.00e+00 positive regulation of GTPase activity 0.00e+00 0.00e+00 small GTPase mediated signal transduction 0.00e+00 0.00e+00 Golgi vesicle transport 0.00e+00 0.00e+00 retrograde vesicle-mediated transport, Golgi to ER 0.00e+00 0.00e+00 Golgi membrane 0.00e+00 0.00e+00 ARF guanyl-nucleotide exchange factor activity 0.00e+00 0.00e+00 guanyl-nucleotide exchange factor activity 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 5.73e-10 3.15e-07 GTPase activator activity 6.17e-10 3.37e-07 enzyme activator activity 1.48e-09 7.64e-07 GTPase regulator activity 1.71e-07 9.27e-05 protein localization to organelle

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 1.02e-07 1.99e-05 COPI MEDIATED TRANSPORT 5.72e-06 1.14e-03 COPI MEDIATED TRANSPORT 2.60e-04 3.01e-02 SYNTHESIS OF PIPS AT THE GOLGI MEMBRANE 4.37e-04 4.80e-02 MEMBRANE TRAFFICKING 6.14e-04 7.70e-02 SYNTHESIS OF PIPS AT THE GOLGI MEMBRANE 2.34e-03 2.14e-01 PI METABOLISM 2.84e-03 2.53e-01 ACTIVATION OF CHAPERONE GENES BY XBP1S 3.20e-03 2.81e-01 TRANS GOLGI NETWORK VESICLE BUDDING 4.14e-03 3.91e-01 PI METABOLISM 4.48e-03 4.17e-01 MEMBRANE TRAFFICKING 5.23e-03 4.74e-01 ACTIVATION OF CHAPERONE GENES BY XBP1S 6.15e-03 4.89e-01 UNFOLDED PROTEIN RESPONSE 8.94e-03 7.32e-01 UNFOLDED PROTEIN RESPONSE 9.87e-03 7.93e-01 TRANS GOLGI NETWORK VESICLE BUDDING 1.13e-02 8.10e-01 DIABETES PATHWAYS 1.63e-02 1.00e+00 ASSOCIATION OF TRIC CCT WITH TARGET PROTEINS DURING BIOSYNTHESIS 2.00e-02 1.00e+00 LYSOSOME VESICLE BIOGENESIS 2.15e-02 1.00e+00 NEF MEDIATES DOWN MODULATION OF CELL SURFACE RECEPTORS BY RECRUITING THEM TO CLATHRIN ADAPTERS 2.88e-02 1.00e+00 NEF MEDIATES DOWN MODULATION OF CELL SURFACE RECEPTORS BY RECRUITING THEM TO CLATHRIN ADAPTERS 2.98e-02 1.00e+00 PROTEIN FOLDING

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 4.36e-04 5.6e-01 small hippocampus 1.87e-03 1.0e+00 absent NK T cells 1.88e-03 1.0e+00 macrocytic anemia 3.74e-03 1.0e+00 absent photoreceptor inner segment 5.61e-03 1.0e+00 abnormal brain ventricular system morphology 5.61e-03 1.0e+00 disorganized photoreceptor inner segment 5.61e-03 1.0e+00 decreased transitional stage T1 B cell number 5.61e-03 1.0e+00 abnormal hepatic cord morphology 6.24e-03 1.0e+00 decreased bone mineral content 8.92e-03 1.0e+00 decreased lean body mass 9.33e-03 1.0e+00 abnormal brain ependyma motile cilium physiology 9.34e-03 1.0e+00 decreased transitional stage T2 B cell number 1.09e-02 1.0e+00 ectopic neuron 1.12e-02 1.0e+00 abnormal sympathetic nervous system physiology 1.12e-02 1.0e+00 abnormal abdominal wall morphology 1.12e-02 1.0e+00 truncated ribs 1.31e-02 1.0e+00 abnormal adipose tissue amount 1.31e-02 1.0e+00 increased leukemia incidence 1.49e-02 1.0e+00 abnormal cranial suture morphology 1.49e-02 1.0e+00 abnormal neutrophil morphology

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

²FDR corrected p-value (Benjamini-Hochberg)