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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod175

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod175 Module size 28 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 140766 ADAMTS14 ADAM metallopeptidase with thrombospondin type 1 motif 14 9509 ADAMTS2 ADAM metallopeptidase with thrombospondin type 1 motif 2 9508 ADAMTS3 ADAM metallopeptidase with thrombospondin type 1 motif 3 9719 ADAMTSL2 ADAMTS like 2 339366 ADAMTSL5 ADAMTS like 5 649 BMP1 bone morphogenetic protein 1 134553 C5orf24 chromosome 5 open reading frame 24 2202 EFEMP1 EGF containing fibulin extracellular matrix protein 1 30008 EFEMP2 EGF containing fibulin extracellular matrix protein 2 100130933 ELN small integral membrane protein 6 2192 FBLN1 fibulin 1 2199 FBLN2 fibulin 2 10516 FBLN5 fibulin 5 2200 FBN1 fibrillin 1 2201 FBN2 fibrillin 2 4015 LOX lysyl oxidase 4016 LOXL1 lysyl oxidase like 1 4053 LTBP2 latent transforming growth factor beta binding protein 2 4237 MFAP2 microfibril associated protein 2 4238 MFAP3 microfibril associated protein 3 4239 MFAP4 microfibril associated protein 4 8076 MFAP5 microfibril associated protein 5 5118 PCOLCE procollagen C-endopeptidase enhancer 26577 PCOLCE2 procollagen C-endopeptidase enhancer 2 167681 PRSS35 serine protease 35 7837 PXDN peroxidasin 137902 PXDNL peroxidasin like 7092 TLL1 tolloid like 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 3.39e-01 1.35e-15 Reactome Crosslinking of collagen fibrils Extracellular matrix organization 3.09e-01 1.11e-13 GO extracellular matrix constituent conferring elasticity molecular_function 2.00e-01 1.35e-15 GO microfibril cellular_component 9.80e-02 1.90e-34 Reactome Elastic fibre formation Extracellular matrix organization 8.19e-02 2.92e-09 GO supramolecular fiber organization biological_process 7.70e-02 3.67e-07 GO peptidase activator activity molecular_function 7.06e-02 5.17e-10 GO embryonic eye morphogenesis biological_process 6.02e-02 2.55e-22 Reactome Molecules associated with elastic fibres Extracellular matrix organization 3.95e-02 5.17e-10 GO elastic fiber assembly biological_process 2.57e-02 2.23e-09 Reactome Defective B3GALTL causes Peters-plus syndrome (PpS) Disease 1.28e-03 2.94e-09 Reactome O-glycosylation of TSR domain-containing proteins 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 extracellular structure organization 0.00e+00 0.00e+00 extracellular matrix organization 0.00e+00 0.00e+00 extracellular matrix 0.00e+00 0.00e+00 proteinaceous extracellular matrix 0.00e+00 0.00e+00 microfibril 0.00e+00 0.00e+00 extracellular matrix structural constituent 3.11e-10 1.50e-07 elastic fiber 3.75e-09 2.58e-06 embryonic eye morphogenesis 1.65e-08 7.27e-06 metalloendopeptidase activity 2.64e-08 1.12e-05 calcium ion binding 3.83e-08 2.30e-05 post-embryonic eye morphogenesis 8.82e-08 5.03e-05 post-embryonic animal organ morphogenesis 1.09e-07 6.12e-05 extracellular matrix disassembly 1.25e-07 6.95e-05 collagen fibril organization 1.65e-07 8.98e-05 supramolecular fiber organization 4.32e-07 1.47e-04 metallopeptidase activity 5.48e-07 1.82e-04 heparin binding 8.64e-07 4.16e-04 post-embryonic animal organ development 1.79e-06 8.11e-04 elastic fiber assembly 1.81e-06 5.47e-04 glycosaminoglycan binding

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 7.00e-11 1.94e-08 COLLAGEN FORMATION 1.13e-10 4.08e-08 COLLAGEN FORMATION 1.10e-09 2.66e-07 EXTRACELLULAR MATRIX ORGANIZATION 4.53e-09 1.37e-06 EXTRACELLULAR MATRIX ORGANIZATION 7.23e-03 5.62e-01 HDL MEDIATED LIPID TRANSPORT 1.99e-02 1.00e+00 LIPOPROTEIN METABOLISM 2.74e-02 1.00e+00 INTEGRIN CELL SURFACE INTERACTIONS 2.96e-02 1.00e+00 HDL MEDIATED LIPID TRANSPORT 4.51e-02 1.00e+00 LIPID DIGESTION MOBILIZATION AND TRANSPORT 4.62e-02 1.00e+00 LIPOPROTEIN METABOLISM

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 8.05e-09 2.21e-04 abnormal cutaneous elastic fiber morphology 6.59e-08 1.03e-03 emphysema 1.79e-07 2.26e-03 loose skin 5.86e-07 5.96e-03 abnormal cutaneous collagen fibril morphology 5.41e-06 3.12e-02 overexpanded pulmonary alveoli 5.72e-06 3.17e-02 abnormal aorta elastic tissue morphology 1.09e-05 5.02e-02 abnormal aorta wall morphology 1.33e-05 5.71e-02 abnormal aorta elastic fiber morphology 1.96e-05 7.47e-02 aortic aneurysm 6.06e-05 1.62e-01 diaphragmatic hernia 8.42e-05 2.03e-01 abnormal blood vessel elastic tissue morphology 8.85e-05 2.09e-01 abnormal descending thoracic aorta morphology 1.49e-04 2.94e-01 abnormal ascending aorta morphology 1.59e-04 3.06e-01 abnormal hypodermis morphology 2.09e-04 3.58e-01 abnormal aorta morphology 3.47e-04 4.88e-01 increased aorta wall thickness 5.21e-04 6.20e-01 hemothorax 8.25e-04 8.06e-01 abnormal aorta smooth muscle morphology 9.99e-04 9.02e-01 ostium primum atrial septal defect 1.08e-03 9.40e-01 abnormal tendon morphology

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

²FDR corrected p-value (Benjamini-Hochberg)