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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod23

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod23 Module size 61 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 49 ACR acrosin 566 AZU1 azurocidin 1 1990 CELA1 chymotrypsin like elastase family member 1 63036 CELA2A chymotrypsin like elastase family member 2A 51032 CELA2B chymotrypsin like elastase family member 2B 23436 CELA3B chymotrypsin like elastase family member 3B 1215 CMA1 chymase 1 1504 CTRB1 chymotrypsinogen B1 440387 CTRB2 chymotrypsinogen B2 11330 CTRC chymotrypsin C 1506 CTRL chymotrypsin like 90338 F11 zinc finger protein 160 2155 F7 coagulation factor VII 2158 F9 coagulation factor IX 2999 GZMH granzyme H 3004 GZMM granzyme M 3026 HABP2 hyaluronan binding protein 2 3249 HPN hepsin 3250 HPR haptoglobin-related protein 3816 KLK1 kallikrein 1 5655 KLK10 kallikrein related peptidase 10 11012 KLK11 kallikrein related peptidase 11 43849 KLK12 kallikrein related peptidase 12 26085 KLK13 kallikrein related peptidase 13 43847 KLK14 kallikrein related peptidase 14 55554 KLK15 kallikrein related peptidase 15 3817 KLK2 kallikrein related peptidase 2 9622 KLK4 kallikrein related peptidase 4 25818 KLK5 kallikrein related peptidase 5 5653 KLK6 kallikrein related peptidase 6 11202 KLK8 kallikrein related peptidase 8 284366 KLK9 kallikrein related peptidase 9 3818 KLKB1 kallikrein B1 10942 PRSS21 serine protease 21 64063 PRSS22 serine protease 22 83886 PRSS27 serine protease 27 260429 PRSS33 serine protease 33 136242 PRSS37 serine protease 37 339501 PRSS38 serine protease 38 339906 PRSS42 serine protease 42 377047 PRSS45 serine protease 45 100287362 PRSS46 serine protease 46, pseudogene 345062 PRSS48 serine protease 48 29122 PRSS50 serine protease 50 203074 PRSS55 serine protease 55 400668 PRSS57 serine protease 57 136541 PRSS58 serine protease 58 5652 PRSS8 serine protease 8 339967 TMPRSS11A transmembrane serine protease 11A 132724 TMPRSS11B transmembrane serine protease 11B 9407 TMPRSS11D transmembrane serine protease 11D 28983 TMPRSS11E transmembrane serine protease 11E 389208 TMPRSS11F transmembrane serine protease 11F 283471 TMPRSS12 transmembrane serine protease 12 84000 TMPRSS13 transmembrane serine protease 13 56649 TMPRSS3 transmembrane serine protease 4 56649 TMPRSS4 transmembrane serine protease 4 80975 TMPRSS5 transmembrane serine protease 5 7177 TPSAB1 tryptase alpha/beta 1 23430 TPSD1 tryptase delta 1 25823 TPSG1 tryptase gamma 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 4.45e-01 2.97e-03 Reactome Acrosome Reaction Reproduction 2.29e-01 1.78e-39 GO serine-type peptidase activity molecular_function 1.00e-01 8.59e-05 Reactome Extrinsic Pathway of Fibrin Clot Formation Hemostasis 8.42e-02 1.97e-23 GO secretory granule cellular_component 4.29e-02 6.91e-06 GO positive regulation of G-protein coupled receptor protein signaling pathway biological_process 3.46e-02 1.63e-05 GO blood coagulation, intrinsic pathway biological_process 2.44e-02 1.22e-07 GO zymogen activation biological_process 2.23e-02 3.52e-10 Reactome Activation of Matrix Metalloproteinases Extracellular matrix organization 1.83e-02 1.55e-06 GO extrinsic component of plasma membrane cellular_component 1.73e-02 2.65e-06 GO anchored component of plasma membrane cellular_component 1.07e-02 2.26e-09 Reactome Formation of the cornified envelope Developmental Biology 2.35e-04 4.67e-04 GO plasminogen 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 0.00e+00 0.00e+00 protein maturation 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 2.01e-11 1.78e-08 protein processing 2.23e-10 1.79e-07 extracellular matrix disassembly 1.70e-09 1.23e-06 cornification 1.46e-07 8.01e-05 keratinization 1.77e-07 5.77e-05 anchored component of plasma membrane 3.02e-07 1.58e-04 keratinocyte differentiation 4.04e-07 2.06e-04 blood coagulation, fibrin clot formation 6.23e-07 3.08e-04 epidermal cell differentiation 1.24e-06 5.78e-04 extracellular matrix organization 1.27e-06 5.91e-04 extracellular structure organization 2.06e-06 9.23e-04 skin development 4.40e-06 1.84e-03 epidermis development 9.76e-06 2.40e-03 anchored component of membrane 1.28e-05 4.83e-03 blood coagulation, intrinsic pathway

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 DEGRADATION OF THE EXTRACELLULAR MATRIX 6.49e-11 1.81e-08 DEGRADATION OF THE EXTRACELLULAR MATRIX 2.26e-10 7.96e-08 EXTRACELLULAR MATRIX ORGANIZATION 8.08e-08 2.11e-05 FORMATION OF FIBRIN CLOT CLOTTING CASCADE 1.04e-07 2.03e-05 EXTRACELLULAR MATRIX ORGANIZATION 2.99e-07 5.55e-05 FORMATION OF FIBRIN CLOT CLOTTING CASCADE 1.47e-06 3.23e-04 INTRINSIC PATHWAY 8.55e-06 1.29e-03 INTRINSIC PATHWAY 4.49e-05 7.60e-03 GAMMA CARBOXYLATION TRANSPORT AND AMINO TERMINAL CLEAVAGE OF PROTEINS 1.14e-04 1.43e-02 GAMMA CARBOXYLATION TRANSPORT AND AMINO TERMINAL CLEAVAGE OF PROTEINS 6.70e-04 8.30e-02 PTM GAMMA CARBOXYLATION HYPUSINE FORMATION AND ARYLSULFATASE ACTIVATION 2.32e-03 2.12e-01 PTM GAMMA CARBOXYLATION HYPUSINE FORMATION AND ARYLSULFATASE ACTIVATION 2.06e-02 1.00e+00 POST TRANSLATIONAL PROTEIN MODIFICATION 2.96e-02 1.00e+00 BMAL1 CLOCK NPAS2 ACTIVATES CIRCADIAN EXPRESSION 3.22e-02 1.00e+00 SIGNALING BY SCF KIT 3.48e-02 1.00e+00 SIGNALING BY SCF KIT 3.80e-02 1.00e+00 CIRCADIAN CLOCK

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 3.15e-05 1.06e-01 increased partial thromboplastin time 1.89e-04 3.36e-01 short vibrissae 7.79e-04 7.78e-01 abnormal epidermis stratum corneum morphology 3.22e-03 1.00e+00 internal hemorrhage 3.60e-03 1.00e+00 impaired skin barrier function 3.75e-03 1.00e+00 kinked vibrissae 3.75e-03 1.00e+00 absent vestibular hair cells 4.48e-03 1.00e+00 abnormal sperm physiology 5.61e-03 1.00e+00 absent cochlear outer hair cells 5.65e-03 1.00e+00 hematoma 5.65e-03 1.00e+00 decreased thyroxine level 5.94e-03 1.00e+00 abnormal blood coagulation 7.48e-03 1.00e+00 short hair 7.48e-03 1.00e+00 abnormal cochlear outer hair cell physiology 7.48e-03 1.00e+00 abnormal cochlear inner hair cell physiology 9.34e-03 1.00e+00 enlarged tectorial membrane 9.35e-03 1.00e+00 vestibular hair cell degeneration 1.12e-02 1.00e+00 abnormal cochlear ganglion morphology 1.12e-02 1.00e+00 abnormal kinocilium morphology 1.12e-02 1.00e+00 absent cochlear hair cells

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

²FDR corrected p-value (Benjamini-Hochberg)