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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod125

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod125 Module size 16 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 293522 AHSP alpha hemoglobin stabilizing protein 3039 HBA1 hemoglobin subunit alpha 1 3040 HBA2 hemoglobin subunit alpha 2 3043 HBB hemoglobin subunit beta 3045 HBD hemoglobin subunit delta 3046 HBE1 hemoglobin subunit epsilon 1 3047 HBG1 hemoglobin subunit gamma 1 3048 HBG2 hemoglobin subunit gamma 2 3042 HBM hemoglobin subunit mu 3049 HBQ1 hemoglobin subunit theta 1 3050 HBZ hemoglobin subunit zeta 23764 MAFF MAF bZIP transcription factor F 4097 MAFG MAF bZIP transcription factor G 7975 MAFK MAF bZIP transcription factor K 4778 NFE2 nuclear factor, erythroid 2 317671 RFESD Rieske Fe-S domain containing

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 2.98e-01 1.40e-29 GO haptoglobin binding molecular_function 2.43e-01 3.23e-31 GO hemoglobin complex cellular_component 1.19e-01 1.40e-28 GO haptoglobin-hemoglobin complex cellular_component 1.18e-01 1.40e-28 GO organic acid binding molecular_function 7.76e-03 9.99e-27 GO oxygen carrier activity 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 0.00e+00 0.00e+00 wound healing 0.00e+00 0.00e+00 oxygen transport 0.00e+00 0.00e+00 coagulation 0.00e+00 0.00e+00 response to wounding 0.00e+00 0.00e+00 regulation of body fluid levels 0.00e+00 0.00e+00 blood coagulation 0.00e+00 0.00e+00 hemostasis 0.00e+00 0.00e+00 hemoglobin complex 0.00e+00 0.00e+00 oxygen binding 0.00e+00 0.00e+00 iron ion binding 0.00e+00 0.00e+00 oxygen transporter activity 0.00e+00 0.00e+00 heme binding 6.83e-09 3.18e-06 hemoglobin binding 1.06e-07 3.61e-05 blood microparticle 4.06e-06 1.07e-03 haptoglobin-hemoglobin complex 7.52e-06 2.99e-03 protein heterooligomerization 5.15e-05 1.09e-02 endocytic vesicle lumen 1.34e-04 3.75e-02 hydrogen peroxide catabolic process 2.07e-04 5.39e-02 regulation of epidermal cell differentiation 3.29e-04 7.94e-02 hydrogen peroxide metabolic process

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 0.0e+00 0.00e+00 FACTORS INVOLVED IN MEGAKARYOCYTE DEVELOPMENT AND PLATELET PRODUCTION 2.8e-10 7.29e-08 FACTORS INVOLVED IN MEGAKARYOCYTE DEVELOPMENT AND PLATELET PRODUCTION

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 3.36e-04 4.8e-01 thrombocytopenia 1.50e-03 1.0e+00 anemia 1.87e-03 1.0e+00 abnormal mean corpuscular hemoglobin 1.87e-03 1.0e+00 increased compact bone mass 1.88e-03 1.0e+00 poikilocytosis 3.36e-03 1.0e+00 partial prenatal lethality 3.74e-03 1.0e+00 abnormal hemoglobin 3.75e-03 1.0e+00 abnormal megakaryocyte differentiation 5.61e-03 1.0e+00 microcytosis 5.62e-03 1.0e+00 anisocytosis 5.62e-03 1.0e+00 abnormal megakaryocyte morphology 5.62e-03 1.0e+00 abnormal hematopoietic system physiology 7.48e-03 1.0e+00 polychromatophilia 9.34e-03 1.0e+00 increased osteoblast cell number 9.34e-03 1.0e+00 increased trabecular bone volume 9.36e-03 1.0e+00 increased megakaryocyte cell number 1.30e-02 1.0e+00 increased incidence of induced tumors 1.31e-02 1.0e+00 increased osteoclast cell number 1.86e-02 1.0e+00 thrombocytosis 2.42e-02 1.0e+00 internal hemorrhage

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

²FDR corrected p-value (Benjamini-Hochberg)