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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod270

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod270 Module size 15 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 8722 CTSF cathepsin F 3108 HLA-DMA major histocompatibility complex, class II, DM alpha 3109 HLA-DMB major histocompatibility complex, class II, DM beta 3111 HLA-DOA major histocompatibility complex, class II, DO alpha 3112 HLA-DOB major histocompatibility complex, class II, DO beta 3113 HLA-DPA1 major histocompatibility complex, class II, DP alpha 1 3125 HLA-DPB1 major histocompatibility complex, class II, DR beta 3 3117 HLA-DQA1 major histocompatibility complex, class II, DQ alpha 1 3118 HLA-DQA2 major histocompatibility complex, class II, DQ alpha 2 2775 HLA-DQB1 G protein subunit alpha o1 3120 HLA-DQB2 major histocompatibility complex, class II, DQ beta 2 3122 HLA-DRA major histocompatibility complex, class II, DR alpha 3123 HLA-DRB1 major histocompatibility complex, class II, DR beta 1 3127 HLA-DRB5 major histocompatibility complex, class II, DR beta 5 931 MS4A1 membrane spanning 4-domains A1

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 4.02e-01 4.97e-40 GO MHC class II protein complex cellular_component 2.15e-01 1.54e-24 GO MHC class II receptor activity molecular_function 7.93e-02 8.39e-19 GO MHC class II protein complex binding molecular_function 8.77e-03 4.35e-23 Reactome Translocation of ZAP-70 to Immunological synapse Immune System

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 regulation of cell-cell adhesion 0e+00 0e+00 positive regulation of cell-cell adhesion 0e+00 0e+00 positive regulation of cell adhesion 0e+00 0e+00 antigen receptor-mediated signaling pathway 0e+00 0e+00 positive regulation of T cell activation 0e+00 0e+00 immune response-activating signal transduction 0e+00 0e+00 antigen processing and presentation of peptide antigen 0e+00 0e+00 antigen processing and presentation 0e+00 0e+00 positive regulation of immune response 0e+00 0e+00 antigen processing and presentation of exogenous peptide antigen via MHC class II 0e+00 0e+00 T cell receptor signaling pathway 0e+00 0e+00 regulation of lymphocyte activation 0e+00 0e+00 interferon-gamma-mediated signaling pathway 0e+00 0e+00 T cell costimulation 0e+00 0e+00 response to interferon-gamma 0e+00 0e+00 lymphocyte costimulation 0e+00 0e+00 antigen processing and presentation of peptide antigen via MHC class II 0e+00 0e+00 immune response-regulating cell surface receptor signaling pathway 0e+00 0e+00 antigen processing and presentation of peptide or polysaccharide antigen via MHC class II 0e+00 0e+00 immune response-activating cell surface receptor signaling pathway

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 MHC CLASS II ANTIGEN PRESENTATION 0.00e+00 0.00e+00 MHC CLASS II ANTIGEN PRESENTATION 5.12e-11 1.44e-08 TRANSLOCATION OF ZAP 70 TO IMMUNOLOGICAL SYNAPSE 6.64e-11 1.84e-08 PHOSPHORYLATION OF CD3 AND TCR ZETA CHAINS 1.44e-10 3.88e-08 PD1 SIGNALING 1.01e-09 2.46e-07 GENERATION OF SECOND MESSENGER MOLECULES 1.10e-09 3.62e-07 TRANSLOCATION OF ZAP 70 TO IMMUNOLOGICAL SYNAPSE 2.72e-09 8.45e-07 PHOSPHORYLATION OF CD3 AND TCR ZETA CHAINS 3.22e-09 9.88e-07 PD1 SIGNALING 2.46e-08 5.17e-06 INTERFERON GAMMA SIGNALING 2.47e-08 6.91e-06 GENERATION OF SECOND MESSENGER MOLECULES 8.38e-08 1.65e-05 DOWNSTREAM TCR SIGNALING 2.20e-07 4.14e-05 TCR SIGNALING 4.54e-07 1.07e-04 DOWNSTREAM TCR SIGNALING 5.33e-07 1.25e-04 INTERFERON GAMMA SIGNALING 1.49e-06 2.52e-04 COSTIMULATION BY THE CD28 FAMILY 2.31e-06 4.89e-04 TCR SIGNALING 7.93e-06 1.54e-03 COSTIMULATION BY THE CD28 FAMILY 8.16e-06 1.24e-03 INTERFERON SIGNALING 1.38e-04 2.07e-02 INTERFERON SIGNALING

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 1.02e-05 4.76e-02 abnormal antigen presentation via MHC class II 2.36e-04 3.88e-01 abnormal level of surface class II molecules 2.62e-04 4.12e-01 decreased CD4-positive, alpha beta T cell number 5.19e-04 6.20e-01 abnormal CD4-positive, alpha beta T cell morphology 1.58e-03 1.00e+00 abnormal CD4-positive, alpha-beta T cell physiology 1.85e-03 1.00e+00 decreased susceptibility to experimental autoimmune encephalomyelitis 2.90e-03 1.00e+00 increased CD8-positive, alpha-beta T cell number 3.58e-03 1.00e+00 increased CD4-positive, alpha beta T cell number 3.99e-03 1.00e+00 abnormal B cell physiology 5.63e-03 1.00e+00 decreased susceptibility to experimental autoimmune myasthenia gravis 5.64e-03 1.00e+00 abnormal artery development 5.64e-03 1.00e+00 increased anti-erythrocyte antigen antibody level 9.36e-03 1.00e+00 abnormal MHC II cell surface expression on macrophages 9.36e-03 1.00e+00 abnormal antigen presentation 9.37e-03 1.00e+00 absent CD4-positive, alpha beta T cells 9.38e-03 1.00e+00 decreased susceptibility to autoimmune disorder 1.28e-02 1.00e+00 abnormal splenocyte physiology 1.31e-02 1.00e+00 abnormal positive T cell selection 1.50e-02 1.00e+00 increased transitional stage B cell number 1.50e-02 1.00e+00 hemolytic anemia

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

²FDR corrected p-value (Benjamini-Hochberg)