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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod155

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod155 Module size 22 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 1650 DDOST dolichyl-diphosphooligosaccharide--protein glycosyltransferase non-catalytic subunit 6184 RPN1 ribophorin I 6185 RPN2 ribophorin II 23478 SEC11A SEC11 homolog A, signal peptidase complex subunit 90701 SEC11C SEC11 homolog C, signal peptidase complex subunit 10952 SEC61B Sec61 translocon beta subunit 23480 SEC61G Sec61 translocon gamma subunit 28972 SPCS1 signal peptidase complex subunit 1 9789 SPCS2 signal peptidase complex subunit 2 60559 SPCS3 signal peptidase complex subunit 3 296076 SRP14 signal recognition particle 14 291685 SRP19 signal recognition particle 19 116650 SRP54 signal recognition particle 54A 6730 SRP68 signal recognition particle 68 100909747 SRP72 signal recognition particle 72 kDa protein-like 6726 SRP9 signal recognition particle 9 6734 SRPR SRP receptor subunit alpha 308821 SRPRB RAB30, member RAS oncogene family 6745 SSR1 signal sequence receptor subunit 1 6746 SSR2 signal sequence receptor subunit 2 6747 SSR3 signal sequence receptor subunit 3 312903 TRAM1 translocation associated membrane protein 1

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 2.09e-18 GO signal recognition particle, endoplasmic reticulum targeting cellular_component 1.41e-01 1.18e-13 Reactome Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) Metabolism of proteins 1.41e-01 1.18e-13 Reactome Synthesis, secretion, and inactivation of Glucose-dependent Insulinotropic Polypeptide (GIP) Metabolism of proteins 1.29e-01 5.31e-13 GO cotranslational protein targeting to membrane biological_process 1.22e-01 1.52e-07 GO dolichyl-diphosphooligosaccharide-protein glycotransferase activity molecular_function 1.20e-01 1.46e-17 GO 7S RNA binding molecular_function 8.59e-02 9.72e-13 GO signal peptide processing biological_process 7.25e-02 6.95e-46 Reactome SRP-dependent cotranslational protein targeting to membrane Metabolism of proteins 7.09e-02 9.64e-16 GO protein targeting to ER biological_process 4.70e-02 9.72e-13 Reactome Synthesis, secretion, and deacylation of Ghrelin Metabolism of proteins

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 protein targeting to ER 0.00e+00 0.00e+00 protein targeting to membrane 0.00e+00 0.00e+00 establishment of protein localization to membrane 0.00e+00 0.00e+00 establishment of protein localization to organelle 0.00e+00 0.00e+00 protein targeting 0.00e+00 0.00e+00 cotranslational protein targeting to membrane 0.00e+00 0.00e+00 SRP-dependent cotranslational protein targeting to membrane 0.00e+00 0.00e+00 protein localization to membrane 0.00e+00 0.00e+00 protein localization to endoplasmic reticulum 0.00e+00 0.00e+00 establishment of protein localization to endoplasmic reticulum 0.00e+00 0.00e+00 protein localization to organelle 0.00e+00 0.00e+00 signal recognition particle, endoplasmic reticulum targeting 0.00e+00 0.00e+00 signal peptidase complex 0.00e+00 0.00e+00 7S RNA binding 1.63e-12 1.50e-09 SRP-dependent cotranslational protein targeting to membrane, translocation 3.40e-11 2.16e-08 signal recognition particle binding 6.12e-10 4.68e-07 signal peptide processing 6.90e-10 5.23e-07 protein transmembrane transport 1.14e-09 5.99e-07 ribonucleoprotein complex binding 4.56e-09 2.18e-06 endoplasmic reticulum signal peptide binding

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 SRP DEPENDENT COTRANSLATIONAL PROTEIN TARGETING TO MEMBRANE 0.00e+00 0.00e+00 TRANSLATION 0.00e+00 0.00e+00 SRP DEPENDENT COTRANSLATIONAL PROTEIN TARGETING TO MEMBRANE 0.00e+00 0.00e+00 TRANSLATION 4.28e-09 1.30e-06 SYNTHESIS SECRETION AND DEACYLATION OF GHRELIN 4.30e-09 1.31e-06 SYNTHESIS SECRETION AND INACTIVATION OF GIP 4.35e-09 1.32e-06 DIABETES PATHWAYS 1.19e-08 3.45e-06 SYNTHESIS SECRETION AND INACTIVATION OF GLP1 1.40e-08 4.02e-06 INCRETIN SYNTHESIS SECRETION AND INACTIVATION 3.39e-08 7.03e-06 SYNTHESIS SECRETION AND DEACYLATION OF GHRELIN 4.39e-08 8.94e-06 SYNTHESIS SECRETION AND INACTIVATION OF GIP 6.10e-08 1.22e-05 SYNTHESIS SECRETION AND INACTIVATION OF GLP1 1.33e-07 2.55e-05 DIABETES PATHWAYS 1.61e-07 3.07e-05 INCRETIN SYNTHESIS SECRETION AND INACTIVATION 2.45e-06 5.15e-04 REGULATION OF INSULIN SECRETION 8.29e-06 1.61e-03 INTEGRATION OF ENERGY METABOLISM 4.63e-05 6.22e-03 REGULATION OF INSULIN SECRETION 1.43e-04 1.76e-02 INTEGRATION OF ENERGY METABOLISM 6.20e-04 6.56e-02 ACTIVATION OF CHAPERONE GENES BY XBP1S 1.01e-03 1.19e-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 3.74e-03 1e+00 abnormal placenta physiology 3.74e-03 1e+00 increased placenta apoptosis 3.75e-03 1e+00 abnormal truncus arteriosus septation 3.75e-03 1e+00 abnormal semilunar valve morphology 3.76e-03 1e+00 dilated heart right ventricle 7.47e-03 1e+00 abnormal cardiac epithelial to mesenchymal transition 1.12e-02 1e+00 persistent truncus arteriosis 1.12e-02 1e+00 abnormal interventricular septum morphology 1.13e-02 1e+00 dilated heart left ventricle 1.49e-02 1e+00 decreased placenta weight 1.88e-02 1e+00 enlarged heart 2.23e-02 1e+00 abnormal placenta vasculature 2.24e-02 1e+00 double outlet right ventricle 2.24e-02 1e+00 abnormal heart ventricle morphology 2.45e-02 1e+00 edema 2.58e-02 1e+00 decreased placental labyrinth size 2.59e-02 1e+00 small placenta 2.60e-02 1e+00 decreased fetal weight 2.60e-02 1e+00 fetal growth retardation 2.63e-02 1e+00 abnormal heart development

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

²FDR corrected p-value (Benjamini-Hochberg)