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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod365

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod365 Module size 28 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 9510 ADAMTS1 ADAM metallopeptidase with thrombospondin type 1 motif 1 9507 ADAMTS4 ADAM metallopeptidase with thrombospondin type 1 motif 4 563 AZGP1 alpha-2-glycoprotein 1, zinc-binding 51279 C1RL complement C1r subcomponent like 5688 C6 proteasome subunit alpha 7 9332 CD163 CD163 molecule 51293 CD320 CD320 molecule 63924 CIDEC cell death inducing DFFA like effector c 1584 CPN1 cytochrome P450 family 11 subfamily B member 1 27122 DKK3 dickkopf WNT signaling pathway inhibitor 3 2217 FCGRT Fc fragment of IgG receptor and transporter 53827 FXYD5 FXYD domain containing ion transport regulator 5 84059 GPR98 adhesion G protein-coupled receptor V1 3813 KIR3DS1 killer cell immunoglobulin like receptor, three Ig domains and short cytoplasmic tail 1 3929 LBP lipopolysaccharide binding protein 27076 LYPD3 LY6/PLAUR domain containing 3 4256 MGP matrix Gla protein 9437 NCR1 natural cytotoxicity triggering receptor 1 6134 NOV ribosomal protein L10 55022 PID1 phosphotyrosine interaction domain containing 1 5329 PLAUR plasminogen activator, urokinase receptor 10544 PROCR protein C receptor 9588 PRX peroxiredoxin 6 6407 SEMG2 semenogelin 2 10653 SPINT2 serine peptidase inhibitor, Kunitz type 2 27286 SRPX2 sushi repeat containing protein X-linked 2 4982 TNFRSF11B TNF receptor superfamily member 11b 340348 TSPAN33 tetraspanin 33

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 1.18e-01 3.26e-03 Reactome Defective CD320 causes methylmalonic aciduria Disease 1.18e-01 3.26e-03 Reactome Transfer of LPS from LBP carrier to CD14 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 1.77e-03 2.36e-01 extracellular matrix 1.95e-03 3.34e-01 positive regulation of serine-type endopeptidase activity 2.16e-03 3.01e-01 metallopeptidase activity 2.33e-03 3.85e-01 complement activation, classical pathway 2.60e-03 4.21e-01 humoral immune response mediated by circulating immunoglobulin 2.64e-03 4.27e-01 negative regulation of coagulation 2.90e-03 4.60e-01 humoral immune response 3.17e-03 4.94e-01 acute-phase response 3.50e-03 4.18e-01 cell surface 3.90e-03 5.71e-01 insulin processing 3.95e-03 5.77e-01 leukocyte chemotaxis involved in inflammatory response 4.40e-03 6.27e-01 complement activation 4.44e-03 6.32e-01 retina homeostasis 4.67e-03 5.79e-01 cobalamin transporter activity 4.78e-03 6.71e-01 natural killer cell activation 4.85e-03 5.98e-01 antigen binding 5.50e-03 5.97e-01 proteinaceous extracellular matrix 5.64e-03 6.78e-01 growth factor binding 5.84e-03 7.72e-01 bradykinin catabolic process 5.89e-03 7.74e-01 bone regeneration

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 1.29e-03 1.26e-01 INNATE IMMUNE SYSTEM 9.86e-03 7.92e-01 POST TRANSLATIONAL MODIFICATION SYNTHESIS OF GPI ANCHORED PROTEINS 1.43e-02 1.00e+00 INNATE IMMUNE SYSTEM 1.66e-02 1.00e+00 COMPLEMENT CASCADE 1.69e-02 1.00e+00 TOLL RECEPTOR CASCADES 1.93e-02 1.00e+00 POST TRANSLATIONAL MODIFICATION SYNTHESIS OF GPI ANCHORED PROTEINS 2.96e-02 1.00e+00 COMPLEMENT CASCADE

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 1.15e-04 2.48e-01 calcified artery 5.99e-04 6.74e-01 decreased trabecular bone mass 2.01e-03 1.00e+00 abnormal blood homeostasis 2.01e-03 1.00e+00 abnormal bone remodeling 2.99e-03 1.00e+00 decreased bone volume 3.13e-03 1.00e+00 abnormal skeleton physiology 3.29e-03 1.00e+00 increased kidney weight 3.84e-03 1.00e+00 decreased bone trabecula number 4.34e-03 1.00e+00 abnormal long bone epiphyseal plate morphology 5.57e-03 1.00e+00 abnormal osteoclast physiology 5.61e-03 1.00e+00 barrel chest 5.61e-03 1.00e+00 increased length of long bones 5.61e-03 1.00e+00 calcified aortic valve 5.61e-03 1.00e+00 kidney papillary hypoplasia 6.27e-03 1.00e+00 abnormal osteoblast physiology 7.48e-03 1.00e+00 decreased CD8-positive, alpha-beta memory T cell number 7.48e-03 1.00e+00 abnormal otic capsule morphology 9.33e-03 1.00e+00 abnormal pro-B cell differentiation 9.34e-03 1.00e+00 increased Schwann cell number 9.34e-03 1.00e+00 kidney vascular congestion

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

²FDR corrected p-value (Benjamini-Hochberg)