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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod368

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod368 Module size 3 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 5033 P4HA1 prolyl 4-hydroxylase subunit alpha 1 8974 P4HA2 prolyl 4-hydroxylase subunit alpha 2 283208 P4HA3 prolyl 4-hydroxylase subunit alpha 3

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 1.29e-01 6.63e-11 GO peptidyl-proline hydroxylation to 4-hydroxy-L-proline biological_process 6.18e-02 1.95e-10 GO oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen molecular_function

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 2.53e-08 1.56e-05 peptidyl-proline hydroxylation 2.71e-08 1.67e-05 protein hydroxylation 7.58e-08 2.96e-05 procollagen-proline 4-dioxygenase activity 3.29e-07 1.15e-04 peptidyl-proline 4-dioxygenase activity 3.43e-07 1.19e-04 peptidyl-proline dioxygenase activity 4.22e-07 1.44e-04 oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen 4.24e-07 1.45e-04 oxidoreductase activity, acting on single donors with incorporation of molecular oxygen 1.34e-06 4.16e-04 L-ascorbic acid binding 2.35e-06 6.96e-04 oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors 5.08e-06 1.40e-03 monosaccharide binding 7.19e-06 1.93e-03 vitamin binding 7.25e-06 1.94e-03 iron ion binding 9.31e-06 2.44e-03 dioxygenase activity 9.61e-06 2.52e-03 oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen 1.75e-05 4.07e-03 endoplasmic reticulum lumen 2.96e-05 7.06e-03 carbohydrate binding 8.26e-05 1.76e-02 carboxylic acid binding 8.27e-05 1.76e-02 organic acid binding 2.03e-04 3.82e-02 oxidoreductase activity 1.95e-03 3.34e-01 4-hydroxyproline metabolic process

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

²FDR corrected p-value (Benjamini-Hochberg)