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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod246

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod246 Module size 28 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 400073 C12orf76 chromosome 12 open reading frame 76 60681 FKBP10 FK506 binding protein 10 51303 FKBP11 FK506 binding protein 11 55033 FKBP14 FK506 binding protein 14 2280 FKBP1A FK506 binding protein 1A 2281 FKBP1B FK506 binding protein 1B NA FKBP1C 2286 FKBP2 FK506 binding protein 2 2287 FKBP3 FK506 binding protein 3 63943 FKBP4 FK506 binding protein like 2289 FKBP5 FK506 binding protein 5 8468 FKBP6 FK506 binding protein 6 51661 FKBP7 FK506 binding protein 7 23770 FKBP8 FK506 binding protein 8 2281 FKBP9 FK506 binding protein 1B 125336 LOXHD1 lipoxygenase homology domains 1 54468 MIOS meiosis regulator for oocyte development 152518 NFXL1 nuclear transcription factor, X-box binding like 1 57282 SLC4A10 solute carrier family 4 member 10 83959 SLC4A11 solute carrier family 4 member 11 6522 SLC4A2 solute carrier family 4 member 2 6508 SLC4A3 solute carrier family 4 member 3 8671 SLC4A4 solute carrier family 4 member 4 57835 SLC4A5 solute carrier family 4 member 5 9497 SLC4A7 solute carrier family 4 member 7 9498 SLC4A8 solute carrier family 4 member 8 83697 SLC4A9 solute carrier family 4 member 9 9589 WTAP WT1 associated protein

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 5.08e-01 4.40e-20 GO FK506 binding molecular_function 3.84e-01 5.19e-23 Reactome Bicarbonate transporters Transport of small molecules 2.56e-01 4.97e-18 GO sodium:bicarbonate symporter activity molecular_function 1.47e-01 4.97e-29 GO protein peptidyl-prolyl isomerization biological_process 1.19e-01 2.84e-23 GO inorganic anion exchanger 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 protein peptidyl-prolyl isomerization 0.00e+00 0.00e+00 protein folding 0.00e+00 0.00e+00 chaperone-mediated protein folding 0.00e+00 0.00e+00 inorganic anion transport 0.00e+00 0.00e+00 regulation of pH 0.00e+00 0.00e+00 regulation of cellular pH 0.00e+00 0.00e+00 bicarbonate transport 0.00e+00 0.00e+00 regulation of intracellular pH 0.00e+00 0.00e+00 drug binding 0.00e+00 0.00e+00 macrolide binding 0.00e+00 0.00e+00 peptidyl-prolyl cis-trans isomerase activity 0.00e+00 0.00e+00 FK506 binding 0.00e+00 0.00e+00 isomerase activity 0.00e+00 0.00e+00 inorganic anion exchanger activity 1.12e-11 7.43e-09 anion:anion antiporter activity 7.87e-11 6.60e-08 anion transmembrane transport 1.85e-10 1.09e-07 sodium:bicarbonate symporter activity 1.05e-09 7.81e-07 metal ion transport 4.30e-09 2.07e-06 antiporter activity 4.49e-09 3.06e-06 cellular cation homeostasis

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 1.94e-09 4.58e-07 TRANSPORT OF INORGANIC CATIONS ANIONS AND AMINO ACIDS OLIGOPEPTIDES 2.42e-09 7.57e-07 TRANSPORT OF INORGANIC CATIONS ANIONS AND AMINO ACIDS OLIGOPEPTIDES 1.98e-07 3.74e-05 SLC MEDIATED TRANSMEMBRANE TRANSPORT 2.62e-07 6.42e-05 SLC MEDIATED TRANSMEMBRANE TRANSPORT 9.57e-06 1.84e-03 TRANSMEMBRANE TRANSPORT OF SMALL MOLECULES 9.90e-03 7.27e-01 TGF BETA RECEPTOR SIGNALING IN EMT EPITHELIAL TO MESENCHYMAL TRANSITION 1.09e-02 8.53e-01 TGF BETA RECEPTOR SIGNALING IN EMT EPITHELIAL TO MESENCHYMAL TRANSITION 1.50e-02 1.00e+00 TGF BETA RECEPTOR SIGNALING ACTIVATES SMADS 2.07e-02 1.00e+00 TGF BETA RECEPTOR SIGNALING ACTIVATES SMADS 3.19e-02 1.00e+00 MEIOTIC SYNAPSIS 3.49e-02 1.00e+00 MEIOTIC SYNAPSIS 3.96e-02 1.00e+00 SIGNALING BY TGF BETA RECEPTOR COMPLEX 4.03e-02 1.00e+00 SIGNALING BY TGF BETA RECEPTOR COMPLEX

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 6.02e-07 6.05e-03 abnormal pH regulation 1.78e-04 3.25e-01 abnormal spiral ligament fibrocyte morphology 2.82e-04 4.35e-01 renal tubular acidosis 2.87e-04 4.38e-01 decreased circulating bicarbonate level 6.11e-04 6.81e-01 abnormal renal reabsorbtion 8.25e-04 8.06e-01 increased urine sodium level 1.40e-03 1.00e+00 decreased circulating sodium level 1.84e-03 1.00e+00 abnormal urine homeostasis 2.99e-03 1.00e+00 decreased circulating creatinine level 3.08e-03 1.00e+00 blindness 4.78e-03 1.00e+00 increased systemic arterial diastolic blood pressure 5.61e-03 1.00e+00 abnormal Claudius cell morphology 5.62e-03 1.00e+00 increased urine bicarbonate level 5.64e-03 1.00e+00 coiled cecum 5.68e-03 1.00e+00 abnormal retinal apoptosis 7.03e-03 1.00e+00 decreased urine osmolality 7.52e-03 1.00e+00 small cecum 9.36e-03 1.00e+00 abnormal Descemet membrane 1.12e-02 1.00e+00 increased spinal cord size 1.12e-02 1.00e+00 collapsed Reissner membrane

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

²FDR corrected p-value (Benjamini-Hochberg)