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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod117

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod117 Module size 27 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 372 ARCN1 archain 1 205428 C3orf58 chromosome 3 open reading frame 58 1314 COPA coatomer protein complex subunit alpha 1315 COPB1 coatomer protein complex subunit beta 1 9276 COPB2 coatomer protein complex subunit beta 2 11316 COPE coatomer protein complex subunit epsilon 22820 COPG1 coatomer protein complex subunit gamma 1 22818 COPZ1 coatomer protein complex subunit zeta 1 51226 COPZ2 coatomer protein complex subunit zeta 2 8720 MBTPS1 membrane bound transcription factor peptidase, site 1 10113 PREB prolactin regulatory element binding 56681 SAR1A secretion associated Ras related GTPase 1A 51128 SAR1B secretion associated Ras related GTPase 1B 9047 SCAP SH2 domain containing 2A 6357 SCYL1 C-C motif chemokine ligand 13 10484 SEC23A Sec23 homolog A, coat complex II component 10483 SEC23B Sec23 homolog B, coat complex II component 10802 SEC24A SEC24 homolog A, COPII coat complex component 10427 SEC24B SEC24 homolog B, COPII coat complex component 9632 SEC24C SEC24 homolog C, COPII coat complex component 9871 SEC24D SEC24 homolog D, COPII coat complex component 22872 SEC31A SEC31 homolog A, COPII coat complex component 25956 SEC31B SEC31 homolog B, COPII coat complex component 144108 SPTY2D1 SPT2 chromatin protein domain containing 1 23423 TMED3 transmembrane p24 trafficking protein 3 51014 TMED7 transmembrane p24 trafficking protein 7 501658 VMA21 VMA21 vacuolar H+-ATPase homolog (S. cerevisiae)

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 5.83e-01 5.76e-33 GO COPI vesicle coat cellular_component 3.50e-01 1.85e-29 GO COPII vesicle coat cellular_component 2.39e-01 9.33e-24 GO cargo loading into COPII-coated vesicle biological_process 2.89e-02 1.09e-15 Reactome Regulation of cholesterol biosynthesis by SREBP (SREBF) Metabolism 7.78e-03 4.23e-14 Reactome Cargo concentration in the ER Metabolism of proteins#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 0e+00 0e+00 retrograde vesicle-mediated transport, Golgi to ER 0e+00 0e+00 Golgi vesicle transport 0e+00 0e+00 COPII-coated vesicle budding 0e+00 0e+00 COPII vesicle coating 0e+00 0e+00 vesicle targeting, to, from or within Golgi 0e+00 0e+00 ER to Golgi vesicle-mediated transport 0e+00 0e+00 membrane budding 0e+00 0e+00 vesicle targeting 0e+00 0e+00 membrane coat 0e+00 0e+00 cytoplasmic vesicle membrane 0e+00 0e+00 vesicle membrane 0e+00 0e+00 ER to Golgi transport vesicle membrane 0e+00 0e+00 vesicle coat 0e+00 0e+00 ER to Golgi transport vesicle 0e+00 0e+00 transport vesicle 0e+00 0e+00 coated vesicle 0e+00 0e+00 COPII vesicle coat 0e+00 0e+00 Golgi-associated vesicle 0e+00 0e+00 Golgi-associated vesicle membrane 0e+00 0e+00 COPI-coated vesicle membrane

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 TRANSPORT TO THE GOLGI AND SUBSEQUENT MODIFICATION 0.00e+00 0.00e+00 MEMBRANE TRAFFICKING 0.00e+00 0.00e+00 COPI MEDIATED TRANSPORT 0.00e+00 0.00e+00 MEMBRANE TRAFFICKING 0.00e+00 0.00e+00 COPI MEDIATED TRANSPORT 1.49e-12 5.84e-10 ANTIGEN PRESENTATION FOLDING ASSEMBLY AND PEPTIDE LOADING OF CLASS I MHC 2.87e-11 1.09e-08 ASPARAGINE N LINKED GLYCOSYLATION 1.54e-10 4.13e-08 TRANSPORT TO THE GOLGI AND SUBSEQUENT MODIFICATION 1.94e-09 4.58e-07 ASPARAGINE N LINKED GLYCOSYLATION 4.56e-09 1.38e-06 POST TRANSLATIONAL PROTEIN MODIFICATION 5.75e-09 1.28e-06 ANTIGEN PRESENTATION FOLDING ASSEMBLY AND PEPTIDE LOADING OF CLASS I MHC 3.36e-08 9.22e-06 MHC CLASS II ANTIGEN PRESENTATION 4.00e-08 8.21e-06 MHC CLASS II ANTIGEN PRESENTATION 3.59e-07 6.61e-05 POST TRANSLATIONAL PROTEIN MODIFICATION 1.98e-06 4.23e-04 CLASS I MHC MEDIATED ANTIGEN PROCESSING PRESENTATION 1.36e-04 1.68e-02 CLASS I MHC MEDIATED ANTIGEN PROCESSING PRESENTATION 2.72e-04 3.76e-02 UNFOLDED PROTEIN RESPONSE 1.17e-03 1.16e-01 UNFOLDED PROTEIN RESPONSE 1.23e-03 1.40e-01 DIABETES PATHWAYS 2.90e-03 2.92e-01 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 4.72e-04 5.88e-01 decreased circulating cholesterol level 1.08e-03 9.40e-01 abnormal Purkinje cell dendrite morphology 1.35e-03 1.00e+00 decreased Purkinje cell number 2.38e-03 1.00e+00 decreased circulating LDL cholesterol level 3.74e-03 1.00e+00 abnormal exocrine pancreas physiology 3.74e-03 1.00e+00 decreased pancreatic acinar cell number 3.75e-03 1.00e+00 retroesophageal right subclavian artery 3.85e-03 1.00e+00 abnormal Purkinje cell morphology 4.28e-03 1.00e+00 preweaning lethality 5.61e-03 1.00e+00 abnormal motor nerve collateral sprouting 5.61e-03 1.00e+00 abnormal peripheral nervous system regeneration 7.47e-03 1.00e+00 peripheral nervous system degeneration 7.47e-03 1.00e+00 abnormal sublingual gland morphology 7.48e-03 1.00e+00 abnormal submandibular gland morphology 9.33e-03 1.00e+00 pancreatic acinar hypoplasia 9.33e-03 1.00e+00 abnormal Paneth cell morphology 1.12e-02 1.00e+00 abnormal involuntary movement 1.12e-02 1.00e+00 abnormal cochlear inner hair cell morphology 1.12e-02 1.00e+00 abnormal endocrine pancreas morphology 1.12e-02 1.00e+00 abnormal pancreatic acinus morphology

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

²FDR corrected p-value (Benjamini-Hochberg)