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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod1

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod1 Module size 33 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 712 C1QA complement C1q A chain 713 C1QB complement C1q B chain 714 C1QC complement C1q C chain 715 C1R complement C1r 716 C1S complement C1s 308846 C2 UV radiation resistance associated 720 C4A complement C4A (Rodgers blood group) 721 C4B complement C4B (Chido blood group) 722 C4BPA complement component 4 binding protein alpha 725 C4BPB complement component 4 binding protein beta 4179 CD46 CD46 molecule 975 CD81 CD81 molecule 629 CFB complement factor B 3075 CFH complement factor H 3078 CFHR1 complement factor H related 1 3426 CFI complement factor I 1378 CR1 complement C3b/C4b receptor 1 (Knops blood group) 1380 CR2 complement C3d receptor 2 1465 CRP cysteine and glycine rich protein 1 114784 CSMD2 CUB and Sushi multiple domains 2 114788 CSMD3 CUB and Sushi multiple domains 3 2210 FCGR1B Fc fragment of IgG receptor Ib 2219 FCN1 ficolin 1 2220 FCN2 ficolin 2 8547 FCN3 ficolin 3 5648 MASP1 mannan binding lectin serine peptidase 1 10747 MASP2 mannan binding lectin serine peptidase 2 4153 MBL2 mannose binding lectin 2 4360 MRC1 mannose receptor C-type 1 5738 PTGFRN prostaglandin F2 receptor inhibitor 5806 PTX3 pentraxin 3 6283 S100A12 S100 calcium binding protein A12 283600 SLC25A47 solute carrier family 25 member 47

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 4.78e-01 1.36e-14 Reactome Ficolins bind to repetitive carbohydrate structures on the target cell surface Immune System 2.64e-01 1.30e-10 Reactome Activation of C3 and C5 Immune System 2.04e-01 1.71e-12 GO opsonization biological_process 1.37e-01 5.77e-16 Reactome Lectin pathway of complement activation Immune System 7.74e-02 2.96e-07 GO complement component C1q binding molecular_function 6.46e-02 1.32e-45 Reactome Complement cascade Immune System 5.26e-02 1.23e-32 GO regulation of complement activation 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 0e+00 0e+00 complement activation 0e+00 0e+00 complement activation, lectin pathway 0e+00 0e+00 innate immune response 0e+00 0e+00 humoral immune response 0e+00 0e+00 positive regulation of immune response 0e+00 0e+00 adaptive immune response 0e+00 0e+00 adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains 0e+00 0e+00 leukocyte mediated immunity 0e+00 0e+00 humoral immune response mediated by circulating immunoglobulin 0e+00 0e+00 complement activation, classical pathway 0e+00 0e+00 immunoglobulin mediated immune response 0e+00 0e+00 B cell mediated immunity 0e+00 0e+00 regulation of complement activation 0e+00 0e+00 regulation of acute inflammatory response 0e+00 0e+00 regulation of humoral immune response 0e+00 0e+00 regulation of inflammatory response 0e+00 0e+00 regulation of protein processing 0e+00 0e+00 blood microparticle 0e+00 0e+00 serine hydrolase activity 0e+00 0e+00 endopeptidase activity

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 COMPLEMENT CASCADE 0.00e+00 0.00e+00 INITIAL TRIGGERING OF COMPLEMENT 0.00e+00 0.00e+00 INNATE IMMUNE SYSTEM 0.00e+00 0.00e+00 CREATION OF C4 AND C2 ACTIVATORS 0.00e+00 0.00e+00 REGULATION OF COMPLEMENT CASCADE 0.00e+00 0.00e+00 COMPLEMENT CASCADE 0.00e+00 0.00e+00 INITIAL TRIGGERING OF COMPLEMENT 0.00e+00 0.00e+00 INNATE IMMUNE SYSTEM 0.00e+00 0.00e+00 CREATION OF C4 AND C2 ACTIVATORS 0.00e+00 0.00e+00 REGULATION OF COMPLEMENT CASCADE 1.10e-04 1.69e-02 CROSS PRESENTATION OF SOLUBLE EXOGENOUS ANTIGENS ENDOSOMES 4.05e-03 3.43e-01 CROSS PRESENTATION OF SOLUBLE EXOGENOUS ANTIGENS ENDOSOMES 5.84e-03 5.20e-01 ANTIGEN PROCESSING CROSS PRESENTATION 1.62e-02 1.00e+00 ANTIGEN PROCESSING CROSS PRESENTATION 2.05e-02 1.00e+00 TAK1 ACTIVATES NFKB BY PHOSPHORYLATION AND ACTIVATION OF IKKS COMPLEX 2.59e-02 1.00e+00 ADVANCED GLYCOSYLATION ENDPRODUCT RECEPTOR SIGNALING 2.89e-02 1.00e+00 ADVANCED GLYCOSYLATION ENDPRODUCT RECEPTOR SIGNALING 3.16e-02 1.00e+00 RIP MEDIATED NFKB ACTIVATION VIA DAI 3.57e-02 1.00e+00 TRAF6 MEDIATED NFKB ACTIVATION 4.00e-02 1.00e+00 RIP MEDIATED NFKB ACTIVATION VIA DAI

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 1.35e-06 1.10e-02 increased susceptibility to bacterial infection 3.61e-06 2.28e-02 decreased spleen germinal center size 4.37e-06 2.63e-02 increased susceptibility to bacterial infection induced morbidity/mortality 7.99e-06 4.01e-02 decreased spleen germinal center number 1.34e-05 5.71e-02 abnormal spleen germinal center morphology 1.78e-05 6.99e-02 glomerulonephritis 3.43e-05 1.11e-01 abnormal complement pathway 1.09e-04 2.40e-01 increased anti-nuclear antigen antibody level 1.66e-04 3.13e-01 increased anti-double stranded DNA antibody level 2.57e-04 4.07e-01 cortical renal glomerulopathies 2.94e-04 4.43e-01 decreased vascular permeability 5.42e-04 6.38e-01 abnormal humoral immune response 6.07e-04 6.78e-01 increased anti-single stranded DNA antibody level 6.07e-04 6.78e-01 increased spleen germinal center number 7.38e-04 7.59e-01 decreased B-1a cell number 1.04e-03 9.21e-01 decreased susceptibility to parasitic infection 1.56e-03 1.00e+00 abnormal hippocampus pyramidal cell morphology 1.87e-03 1.00e+00 impaired complement classical pathway 2.09e-03 1.00e+00 abnormal circulating protein level 2.97e-03 1.00e+00 decreased susceptibility to injury

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

²FDR corrected p-value (Benjamini-Hochberg)