Back to main page

DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod114

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod114 Module size 37 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 173 AFM afamin 259 AMBP alpha-1-microglobulin/bikunin precursor 346 APOC4 apolipoprotein C4 350 APOH apolipoprotein H 55937 APOM apolipoprotein M 28834 C7 immunoglobulin lambda constant 7 731 C8A complement C8 alpha chain 732 C8B complement C8 beta chain 733 C8G complement C8 gamma chain 1645 C9 aldo-keto reductase family 1 member C1 7123 CLEC3B C-type lectin domain family 3 member B 1361 CPB2 carboxypeptidase B2 2165 F13B coagulation factor XIII B chain 2147 F2 coagulation factor II, thrombin 26998 FETUB fetuin B 2243 FGA fibrinogen alpha chain 2244 FGB fibrinogen beta chain 2266 FGG fibrinogen gamma chain 2267 FGL1 fibrinogen like 1 10875 FGL2 fibrinogen like 2 2629 GC glucosylceramidase beta 55876 GSDMB gasdermin B 3263 HPX hemopexin 3485 IGFBP2 insulin like growth factor binding protein 2 4018 LPA lipoprotein(a) 11223 MST1L macrophage stimulating 1 like 5004 ORM1 orosomucoid 1 5005 ORM2 orosomucoid 2 308942 PLAT DENN domain containing 5A 5340 PLG plasminogen 55848 PLGRKT plasminogen receptor with a C-terminal lysine 5444 PON1 paraoxonase 1 8858 PROZ protein Z, vitamin K dependent plasma glycoprotein 5858 PZP PZP, alpha-2-macroglobulin like 462 SERPINC1 serpin family C member 1 6694 SPP2 secreted phosphoprotein 2 7448 VTN vitronectin

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 4.49e-01 6.34e-13 Reactome Terminal pathway of complement Immune System 2.08e-01 3.79e-12 GO fibrinogen complex cellular_component 1.37e-01 1.39e-11 GO plasminogen activation biological_process 9.44e-02 3.38e-09 GO negative regulation of fibrinolysis biological_process 7.94e-02 2.07e-12 Reactome Common Pathway of Fibrin Clot Formation Hemostasis 5.73e-02 1.59e-14 GO fibrinolysis biological_process 4.45e-02 3.03e-06 GO platelet dense granule lumen cellular_component 4.42e-02 7.48e-29 GO blood microparticle cellular_component 3.80e-02 1.16e-07 GO high-density lipoprotein particle cellular_component 3.43e-02 1.15e-08 GO protein polymerization biological_process 1.72e-02 6.28e-03 Reactome LDL remodeling Transport of small molecules 1.66e-02 1.19e-04 GO spherical high-density lipoprotein particle cellular_component 1.04e-02 3.85e-11 GO complement activation, alternative pathway biological_process 7.21e-03 2.78e-04 GO positive regulation of tumor necrosis factor secretion 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 0.00e+00 0.00e+00 negative regulation of wound healing 0.00e+00 0.00e+00 regulation of wound healing 0.00e+00 0.00e+00 regulation of response to wounding 0.00e+00 0.00e+00 regulation of blood coagulation 0.00e+00 0.00e+00 negative regulation of blood coagulation 0.00e+00 0.00e+00 fibrinolysis 0.00e+00 0.00e+00 negative regulation of coagulation 0.00e+00 0.00e+00 regulation of proteolysis 0.00e+00 0.00e+00 regulation of protein processing 0.00e+00 0.00e+00 platelet degranulation 0.00e+00 0.00e+00 blood microparticle 2.44e-11 1.32e-08 membrane attack complex 7.00e-11 3.69e-08 fibrinogen complex 1.13e-10 9.32e-08 regulation of humoral immune response 1.76e-10 1.43e-07 plasminogen activation 2.02e-10 1.63e-07 blood coagulation 2.28e-10 1.82e-07 coagulation 2.98e-10 2.36e-07 hemostasis 4.50e-10 3.49e-07 complement activation, alternative pathway 1.11e-09 8.23e-07 regulation of complement activation

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 1.10e-12 3.26e-10 COMMON PATHWAY 1.01e-11 3.89e-09 COMMON PATHWAY 8.50e-10 2.09e-07 FORMATION OF FIBRIN CLOT CLOTTING CASCADE 1.54e-09 4.98e-07 FORMATION OF FIBRIN CLOT CLOTTING CASCADE 5.34e-09 1.20e-06 COMPLEMENT CASCADE 5.46e-08 1.46e-05 COMPLEMENT CASCADE 1.00e-05 1.49e-03 PLATELET AGGREGATION PLUG FORMATION 2.23e-05 3.99e-03 REGULATION OF INSULIN LIKE GROWTH FACTOR IGF ACTIVITY BY INSULIN LIKE GROWTH FACTOR BINDING PROTEINS IGFBPS 2.68e-05 3.75e-03 GAMMA CARBOXYLATION TRANSPORT AND AMINO TERMINAL CLEAVAGE OF PROTEINS 2.77e-05 3.86e-03 GRB2 SOS PROVIDES LINKAGE TO MAPK SIGNALING FOR INTERGRINS 3.54e-05 4.86e-03 P130CAS LINKAGE TO MAPK SIGNALING FOR INTEGRINS 4.57e-05 7.70e-03 PLATELET AGGREGATION PLUG FORMATION 9.02e-05 1.42e-02 P130CAS LINKAGE TO MAPK SIGNALING FOR INTEGRINS 9.02e-05 1.42e-02 GRB2 SOS PROVIDES LINKAGE TO MAPK SIGNALING FOR INTERGRINS 1.13e-04 1.42e-02 REGULATION OF INSULIN LIKE GROWTH FACTOR IGF ACTIVITY BY INSULIN LIKE GROWTH FACTOR BINDING PROTEINS IGFBPS 1.89e-04 2.25e-02 INTEGRIN ALPHAIIB BETA3 SIGNALING 2.56e-04 2.97e-02 INTEGRIN CELL SURFACE INTERACTIONS 2.79e-04 3.85e-02 GAMMA CARBOXYLATION TRANSPORT AND AMINO TERMINAL CLEAVAGE OF PROTEINS 2.87e-04 3.94e-02 RESPONSE TO ELEVATED PLATELET CYTOSOLIC CA2 3.49e-04 3.93e-02 RESPONSE TO ELEVATED PLATELET CYTOSOLIC CA2

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 abnormal blood coagulation 1.39e-05 5.83e-02 thrombosis 4.52e-05 1.33e-01 venoocclusion 6.16e-05 1.63e-01 abnormal circulating fibrinogen level 8.93e-05 2.11e-01 uterine hemorrhage 1.01e-04 2.28e-01 abnormal thrombolysis 1.21e-04 2.55e-01 decreased susceptibility to induced choroidal neovascularization 1.39e-04 2.82e-01 abnormal acute phase protein level 2.53e-04 4.02e-01 hemoperitoneum 5.46e-04 6.41e-01 decreased platelet aggregation 7.44e-04 7.62e-01 abnormal wound healing 1.33e-03 1.00e+00 abnormal microglial cell physiology 1.40e-03 1.00e+00 increased bleeding time 1.70e-03 1.00e+00 pulmonary fibrosis 2.09e-03 1.00e+00 impaired wound healing 2.14e-03 1.00e+00 hemorrhage 2.59e-03 1.00e+00 female infertility 3.75e-03 1.00e+00 absent zona pellucida 5.03e-03 1.00e+00 hepatic necrosis 5.61e-03 1.00e+00 reduced thrombolysis

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

²FDR corrected p-value (Benjamini-Hochberg)