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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod214

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod214 Module size 53 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 81693 AMN amnion associated transmembrane protein 8542 APOL1 apolipoprotein L1 820 CAMP cathelicidin antimicrobial peptide 1041 CDSN corneodesmosin 10136 CELA3A chymotrypsin like elastase family member 3A 1208 CLPS colipase 146225 CMTM2 CKLF like MARVEL transmembrane domain containing 2 1357 CPA1 carboxypeptidase A1 1358 CPA2 carboxypeptidase A2 51200 CPA3 carboxypeptidase A4 51200 CPA4 carboxypeptidase A4 93979 CPA5 carboxypeptidase A5 57094 CPA6 carboxypeptidase A6 1360 CPB1 carboxypeptidase B1 1511 CTSG cathepsin G 50624 CUZD1 CUB and zona pellucida like domains 1 1991 ELANE elastase, neutrophil expressed 83541 F10 family with sequence similarity 110 member A 2161 F12 coagulation factor XII 1272 F3 contactin 1 2157 F8 coagulation factor VIII 2677 GGCX gamma-glutamyl carboxylase 4504 GIF metallothionein 3 2813 GP2 glycoprotein 2 9283 GPR37L1 G protein-coupled receptor 37 like 1 3001 GZMA granzyme A 3002 GZMB granzyme B 3003 GZMK granzyme K 10395 HP DLC1 Rho GTPase activating protein 3818 KLK3 kallikrein B1 5650 KLK7 kallikrein related peptidase 7 140767 NRSN1 neurensin 1 5328 PLAU plasminogen activator, urokinase 5407 PNLIPRP1 pancreatic lipase related protein 1 5547 PRCP prolylcarboxypeptidase 5624 PROC protein C, inactivator of coagulation factors Va and VIIIa 5644 PRSS1 serine protease 1 10279 PRSS16 serine protease 16 5646 PRSS3 serine protease 3 5657 PRTN3 proteinase 3 5967 REG1A regenerating family member 1 alpha 5968 REG1B regenerating family member 1 beta 6035 RNASE1 ribonuclease A family member 1, pancreatic 6690 SPINK1 serine peptidase inhibitor, Kazal type 1 11005 SPINK5 serine peptidase inhibitor, Kazal type 5 342898 SYCN syncollin 6947 TCN1 transcobalamin 1 83639 TEX101 testis expressed 101 7035 TFPI tissue factor pathway inhibitor 7980 TFPI2 tissue factor pathway inhibitor 2 5651 TMPRSS15 transmembrane serine protease 15 7113 TMPRSS2 transmembrane serine protease 2 653808 ZG16 zymogen granule protein 16

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 2.47e-01 2.61e-07 Reactome Extrinsic Pathway of Fibrin Clot Formation Hemostasis 1.64e-01 3.03e-03 Reactome Defective GIF causes intrinsic factor deficiency Disease 1.39e-01 1.73e-12 GO metallocarboxypeptidase activity molecular_function 1.13e-01 2.69e-05 Reactome Defective CUBN causes hereditary megaloblastic anemia 1 Disease 1.02e-01 2.69e-05 Reactome Defective AMN causes hereditary megaloblastic anemia 1 Disease 8.46e-02 1.45e-13 Reactome Formation of Fibrin Clot (Clotting Cascade) Hemostasis 8.08e-02 1.87e-04 Reactome Digestion of dietary lipid Digestion and absorption 7.35e-02 2.93e-15 GO serine-type peptidase activity molecular_function 3.33e-02 3.19e-04 GO positive regulation of immune response biological_process 2.92e-02 1.45e-06 GO cobalamin transport biological_process 2.91e-02 4.10e-09 Reactome Cobalamin (Cbl, vitamin B12) transport and metabolism Metabolism 2.70e-02 4.10e-09 GO cobalamin metabolic process biological_process 2.60e-02 2.45e-05 GO cytolysis biological_process 2.11e-02 4.86e-04 GO zymogen granule membrane cellular_component 1.75e-02 4.86e-04 GO oligosaccharide binding molecular_function 1.06e-02 4.41e-07 GO antimicrobial humoral response biological_process 2.40e-03 1.73e-05 Reactome Metabolism of Angiotensinogen to Angiotensins Metabolism of proteins 1.22e-03 1.43e-05 GO zymogen activation biological_process 7.81e-04 3.09e-06 Reactome Gamma-carboxylation of protein precursors Metabolism of proteins

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 protein processing 0.00e+00 0.00e+00 secretory granule 0.00e+00 0.00e+00 serine hydrolase activity 0.00e+00 0.00e+00 endopeptidase activity 0.00e+00 0.00e+00 serine-type peptidase activity 0.00e+00 0.00e+00 serine-type endopeptidase activity 0.00e+00 0.00e+00 peptidase activity 2.19e-11 1.93e-08 protein maturation 1.12e-10 9.24e-08 blood coagulation 1.34e-10 1.10e-07 coagulation 1.57e-10 1.28e-07 hemostasis 3.38e-10 1.94e-07 carboxypeptidase activity 4.19e-10 3.26e-07 blood coagulation, fibrin clot formation 1.46e-09 7.55e-07 metallocarboxypeptidase activity 4.04e-09 2.77e-06 wound healing 7.37e-09 4.87e-06 cobalamin metabolic process 1.34e-08 8.59e-06 acute inflammatory response 1.64e-08 1.04e-05 antimicrobial humoral response 2.38e-08 1.48e-05 regulation of body fluid levels 2.50e-08 1.55e-05 response to wounding

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 FORMATION OF FIBRIN CLOT CLOTTING CASCADE 0.00e+00 0.00e+00 FORMATION OF FIBRIN CLOT CLOTTING CASCADE 1.99e-07 3.76e-05 INTRINSIC PATHWAY 3.08e-07 7.47e-05 INTRINSIC PATHWAY 7.24e-07 1.29e-04 GAMMA CARBOXYLATION TRANSPORT AND AMINO TERMINAL CLEAVAGE OF PROTEINS 6.11e-06 1.21e-03 GAMMA CARBOXYLATION TRANSPORT AND AMINO TERMINAL CLEAVAGE OF PROTEINS 7.16e-05 9.36e-03 PTM GAMMA CARBOXYLATION HYPUSINE FORMATION AND ARYLSULFATASE ACTIVATION 1.13e-04 1.73e-02 DEGRADATION OF THE EXTRACELLULAR MATRIX 1.43e-04 2.14e-02 PTM GAMMA CARBOXYLATION HYPUSINE FORMATION AND ARYLSULFATASE ACTIVATION 2.96e-04 3.39e-02 DEGRADATION OF THE EXTRACELLULAR MATRIX 3.87e-04 4.31e-02 COMMON PATHWAY 6.05e-04 7.61e-02 COMMON PATHWAY 8.68e-04 1.04e-01 REGULATION OF INSULIN LIKE GROWTH FACTOR IGF ACTIVITY BY INSULIN LIKE GROWTH FACTOR BINDING PROTEINS IGFBPS 2.59e-03 2.34e-01 REGULATION OF INSULIN LIKE GROWTH FACTOR IGF ACTIVITY BY INSULIN LIKE GROWTH FACTOR BINDING PROTEINS IGFBPS 2.62e-03 2.68e-01 EXTRACELLULAR MATRIX ORGANIZATION 4.63e-03 3.85e-01 LIPID DIGESTION MOBILIZATION AND TRANSPORT 7.79e-03 5.98e-01 EXTRACELLULAR MATRIX ORGANIZATION 8.45e-03 7.02e-01 LIPID DIGESTION MOBILIZATION AND TRANSPORT 1.60e-02 1.00e+00 POST TRANSLATIONAL PROTEIN MODIFICATION 2.06e-02 1.00e+00 POST TRANSLATIONAL PROTEIN MODIFICATION

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 3.90e-05 1.21e-01 thrombosis 4.31e-05 1.29e-01 abnormal blood coagulation 9.02e-05 2.12e-01 abnormal acute phase protein level 1.70e-04 3.18e-01 increased susceptibility to infection induced morbidity/mortality 7.18e-04 7.47e-01 increased susceptibility to induced pancreatitis 9.79e-04 8.93e-01 increased susceptibility to fungal infection 1.79e-03 1.00e+00 abnormal response/metabolism to endogenous compounds 1.97e-03 1.00e+00 abnormal pancreas physiology 2.27e-03 1.00e+00 increased sensitivity to induced morbidity/mortality 3.49e-03 1.00e+00 liver fibrosis 3.57e-03 1.00e+00 decreased susceptibility to bacterial infection induced morbidity/mortality 4.15e-03 1.00e+00 partial embryonic lethality during organogenesis 7.49e-03 1.00e+00 abnormal immune tolerance 7.50e-03 1.00e+00 increased aggression 9.34e-03 1.00e+00 reduced thrombolysis 1.10e-02 1.00e+00 intracranial hemorrhage 1.12e-02 1.00e+00 double outlet right ventricle, ventricular defect committed to aorta 1.12e-02 1.00e+00 sparse vibrissae 1.31e-02 1.00e+00 prostate gland inflammation 1.31e-02 1.00e+00 epidermal desquamation

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

²FDR corrected p-value (Benjamini-Hochberg)