Back to main page

DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod36

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod36 Module size 54 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 103 ADAR adenosine deaminase, RNA specific 567 B2M beta-2-microglobulin 909 CD1A CD1a molecule 911 CD1C CD1c molecule 913 CD1E CD1e molecule 4261 CIITA class II major histocompatibility complex transactivator 10143 CLEC3A C-type lectin domain family 3 member A 2633 GBP1 guanylate binding protein 1 2634 GBP2 guanylate binding protein 2 3077 HFE homeostatic iron regulator 3105 HLA-A major histocompatibility complex, class I, A 3106 HLA-B major histocompatibility complex, class I, B 3107 HLA-C major histocompatibility complex, class I, C 3133 HLA-E major histocompatibility complex, class I, E 3134 HLA-F major histocompatibility complex, class I, F 3135 HLA-G major histocompatibility complex, class I, G 3383 ICAM1 intercellular adhesion molecule 1 3429 IFI27 interferon alpha inducible protein 27 122509 IFI27L1 interferon alpha inducible protein 27 like 1 10437 IFI30 IFI30, lysosomal thiol reductase 3430 IFI35 interferon induced protein 35 2537 IFI6 interferon alpha inducible protein 6 8519 IFITM1 interferon induced transmembrane protein 1 10581 IFITM2 interferon induced transmembrane protein 2 10410 IFITM3 interferon induced transmembrane protein 3 51447 IP6K2 inositol hexakisphosphate kinase 2 3659 IRF1 interferon regulatory factor 1 3660 IRF2 interferon regulatory factor 2 3661 IRF3 interferon regulatory factor 3 3662 IRF4 interferon regulatory factor 4 3663 IRF5 interferon regulatory factor 5 3664 IRF6 interferon regulatory factor 6 3665 IRF7 interferon regulatory factor 7 3394 IRF8 interferon regulatory factor 8 10379 IRF9 interferon regulatory factor 9 3802 KIR2DL1 killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 1 3805 KIR2DL4 killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 4 3811 KIR3DL1 killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 1 3812 KIR3DL2 killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 2 3821 KLRC1 killer cell lectin like receptor C1 3822 KLRC2 killer cell lectin like receptor C2 3823 KLRC3 killer cell lectin like receptor C3 8302 KLRC4 killer cell lectin like receptor C4 3824 KLRD1 killer cell lectin like receptor D1 10859 LILRB1 leukocyte immunoglobulin like receptor B1 10288 LILRB2 leukocyte immunoglobulin like receptor B2 25953 MR1 PNKD, MBL domain containing 4502 MT2A metallothionein 2A 4600 MX2 MX dynamin like GTPase 2 6672 SP100 SP100 nuclear antigen 6773 STAT2 signal transducer and activator of transcription 2 6892 TAPBP TAP binding protein 7412 VCAM1 vascular cell adhesion molecule 1 54739 XAF1 XIAP associated factor 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 3.65e-01 1.48e-22 GO MHC class I protein complex cellular_component 1.79e-01 4.99e-56 GO type I interferon signaling pathway biological_process 1.26e-01 2.43e-06 GO lipopeptide binding molecular_function 1.23e-01 9.96e-45 GO interferon-gamma-mediated signaling pathway biological_process 1.02e-01 1.03e-52 Reactome Interferon alpha/beta signaling Immune System 1.01e-01 1.16e-10 GO response to interferon-alpha biological_process 5.75e-02 9.64e-05 GO MHC class I receptor activity molecular_function 4.72e-02 1.04e-05 GO negative regulation of calcium ion transport biological_process 3.46e-02 2.58e-07 GO MHC class I protein binding molecular_function 2.65e-02 6.10e-10 GO cellular defense response biological_process 2.46e-02 7.40e-20 GO positive regulation of T cell mediated cytotoxicity biological_process 1.62e-02 9.73e-25 Reactome Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell Immune System 5.04e-03 1.97e-41 Reactome Interferon gamma signaling 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 0.00e+00 0.00e+00 response to cytokine 0.00e+00 0.00e+00 response to type I interferon 0.00e+00 0.00e+00 type I interferon signaling pathway 0.00e+00 0.00e+00 defense response to other organism 0.00e+00 0.00e+00 innate immune response 0.00e+00 0.00e+00 cytokine-mediated signaling pathway 0.00e+00 0.00e+00 defense response to virus 0.00e+00 0.00e+00 cellular response to cytokine stimulus 0.00e+00 0.00e+00 cellular response to type I interferon 0.00e+00 0.00e+00 antigen processing and presentation 0.00e+00 0.00e+00 response to interferon-gamma 0.00e+00 0.00e+00 interferon-gamma-mediated signaling pathway 0.00e+00 0.00e+00 cellular response to interferon-gamma 0.00e+00 0.00e+00 antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent 0.00e+00 0.00e+00 MHC class I protein complex 0.00e+00 0.00e+00 antigen binding 0.00e+00 0.00e+00 peptide antigen binding 3.54e-12 2.41e-09 beta-2-microglobulin binding 3.67e-12 3.36e-09 response to other organism 7.26e-12 6.57e-09 response to biotic stimulus

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 INTERFERON ALPHA BETA SIGNALING 0.00e+00 0.00e+00 CYTOKINE SIGNALING IN IMMUNE SYSTEM 0.00e+00 0.00e+00 INTERFERON SIGNALING 0.00e+00 0.00e+00 IMMUNOREGULATORY INTERACTIONS BETWEEN A LYMPHOID AND A NON LYMPHOID CELL 0.00e+00 0.00e+00 INTERFERON GAMMA SIGNALING 0.00e+00 0.00e+00 INTERFERON ALPHA BETA SIGNALING 0.00e+00 0.00e+00 CYTOKINE SIGNALING IN IMMUNE SYSTEM 0.00e+00 0.00e+00 INTERFERON SIGNALING 0.00e+00 0.00e+00 IMMUNOREGULATORY INTERACTIONS BETWEEN A LYMPHOID AND A NON LYMPHOID CELL 0.00e+00 0.00e+00 INTERFERON GAMMA SIGNALING 3.61e-12 1.40e-09 ENDOSOMAL VACUOLAR PATHWAY 2.51e-11 7.24e-09 ENDOSOMAL VACUOLAR PATHWAY 1.83e-09 5.85e-07 ANTIGEN PRESENTATION FOLDING ASSEMBLY AND PEPTIDE LOADING OF CLASS I MHC 2.80e-08 5.85e-06 ANTIGEN PRESENTATION FOLDING ASSEMBLY AND PEPTIDE LOADING OF CLASS I MHC 4.01e-06 6.37e-04 ER PHAGOSOME PATHWAY 6.61e-06 1.30e-03 ER PHAGOSOME PATHWAY 1.83e-05 2.63e-03 ANTIGEN PROCESSING CROSS PRESENTATION 2.06e-05 3.71e-03 ANTIGEN PROCESSING CROSS PRESENTATION 1.52e-04 2.26e-02 TRAF6 MEDIATED IRF7 ACTIVATION 2.03e-04 2.40e-02 TRAF6 MEDIATED IRF7 ACTIVATION

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 0.00e+00 0.00e+00 increased susceptibility to viral infection 2.04e-06 1.49e-02 decreased interferon-alpha secretion 2.68e-06 1.87e-02 decreased level of surface class I molecules 1.66e-05 6.68e-02 abnormal cytotoxic T cell physiology 1.97e-05 7.48e-02 abnormal T cell number 5.94e-05 1.60e-01 abnormal immune system physiology 2.03e-04 3.52e-01 decreased dendritic cell number 3.11e-04 4.59e-01 hemochromatosis 3.53e-04 4.92e-01 increased susceptibility to infection induced morbidity/mortality 4.07e-04 5.37e-01 abnormal B cell physiology 4.18e-04 5.46e-01 decreased plasmacytoid dendritic cell number 6.46e-04 7.03e-01 abnormal lymphocyte physiology 6.80e-04 7.25e-01 abnormal level of surface class II molecules 1.33e-03 1.00e+00 decreased susceptibility to experimental autoimmune encephalomyelitis 1.47e-03 1.00e+00 increased lymphocyte cell number 1.99e-03 1.00e+00 insulitis 2.01e-03 1.00e+00 abnormal response to infection 2.15e-03 1.00e+00 increased susceptibility to viral infection induced morbidity/mortality 3.21e-03 1.00e+00 decreased interferon-beta secretion 3.41e-03 1.00e+00 increased double-positive T cell number

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

²FDR corrected p-value (Benjamini-Hochberg)