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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod243

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod243 Module size 12 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 9061 PAPSS1 3'-phosphoadenosine 5'-phosphosulfate synthase 1 9060 PAPSS2 3'-phosphoadenosine 5'-phosphosulfate synthase 2 10861 SLC26A1 solute carrier family 26 member 1 65012 SLC26A10 solute carrier family 26 member 10 284129 SLC26A11 solute carrier family 26 member 11 1836 SLC26A2 solute carrier family 26 member 2 1811 SLC26A3 solute carrier family 26 member 3 5172 SLC26A4 solute carrier family 26 member 4 375611 SLC26A5 solute carrier family 26 member 5 115111 SLC26A7 solute carrier family 26 member 7 116369 SLC26A8 solute carrier family 26 member 8 115019 SLC26A9 solute carrier family 26 member 9

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 2.78e-01 1.18e-33 GO secondary active sulfate transmembrane transporter activity molecular_function 2.78e-01 1.18e-33 GO oxalate transport biological_process 1.36e-01 2.68e-06 Reactome Metabolism of ingested H2SeO4 and H2SeO3 into H2Se Metabolism 9.08e-02 6.15e-30 GO oxalate transmembrane transporter activity molecular_function 8.40e-02 2.05e-12 GO 3'-phosphoadenosine 5'-phosphosulfate biosynthetic process biological_process 8.27e-02 2.05e-12 Reactome Transport and synthesis of PAPS Metabolism 2.08e-02 3.23e-31 GO sulfate transmembrane transporter activity molecular_function 1.99e-02 3.23e-31 GO sulfate transmembrane transport 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 0e+00 0e+00 inorganic anion transport 0e+00 0e+00 chloride transmembrane transport 0e+00 0e+00 sulfate transmembrane transport 0e+00 0e+00 anion transport 0e+00 0e+00 chloride transport 0e+00 0e+00 regulation of pH 0e+00 0e+00 dicarboxylic acid transport 0e+00 0e+00 anion transmembrane transport 0e+00 0e+00 cellular cation homeostasis 0e+00 0e+00 regulation of cellular pH 0e+00 0e+00 bicarbonate transport 0e+00 0e+00 sulfate transport 0e+00 0e+00 cellular chemical homeostasis 0e+00 0e+00 carboxylic acid transport 0e+00 0e+00 cellular ion homeostasis 0e+00 0e+00 regulation of intracellular pH 0e+00 0e+00 regulation of membrane potential 0e+00 0e+00 ion homeostasis 0e+00 0e+00 oxalate transport 0e+00 0e+00 organic anion transport

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 8.05e-09 1.79e-06 TRANSPORT OF INORGANIC CATIONS ANIONS AND AMINO ACIDS OLIGOPEPTIDES 1.16e-08 3.37e-06 TRANSPORT OF INORGANIC CATIONS ANIONS AND AMINO ACIDS OLIGOPEPTIDES 2.38e-07 5.87e-05 SLC MEDIATED TRANSMEMBRANE TRANSPORT 3.85e-07 7.08e-05 SLC MEDIATED TRANSMEMBRANE TRANSPORT 5.30e-06 1.06e-03 TRANSMEMBRANE TRANSPORT OF SMALL MOLECULES 1.36e-04 1.68e-02 CYTOSOLIC SULFONATION OF SMALL MOLECULES 7.29e-04 8.91e-02 CYTOSOLIC SULFONATION OF SMALL MOLECULES 4.86e-03 4.01e-01 PHASE II CONJUGATION 7.79e-03 6.57e-01 PHASE II CONJUGATION 1.28e-02 8.97e-01 BIOLOGICAL OXIDATIONS 1.54e-02 1.00e+00 BIOLOGICAL OXIDATIONS

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 5.05e-05 1.43e-01 abnormal digestive system physiology 1.90e-03 1.00e+00 cochlear hair cell degeneration 2.02e-03 1.00e+00 organ of Corti degeneration 2.13e-03 1.00e+00 cochlear inner hair cell degeneration 3.36e-03 1.00e+00 abnormal long bone hypertrophic chondrocyte zone 3.75e-03 1.00e+00 dilated scala media 3.76e-03 1.00e+00 abnormal spiral limbus morphology 3.76e-03 1.00e+00 dilated cochlea 4.57e-03 1.00e+00 cochlear outer hair cell degeneration 5.61e-03 1.00e+00 abnormal otoacoustic response 5.62e-03 1.00e+00 decreased cochlear microphonics 5.62e-03 1.00e+00 increased circulating bicarbonate level 5.63e-03 1.00e+00 type I spiral ligament fibrocyte degeneration 5.63e-03 1.00e+00 abnormal cochlear endolymph ionic homeostasis 5.63e-03 1.00e+00 decreased otolith number 5.64e-03 1.00e+00 distended Reissner membrane 5.77e-03 1.00e+00 decreased length of long bones 6.84e-03 1.00e+00 impaired hearing 7.47e-03 1.00e+00 nephrolithiasis 7.49e-03 1.00e+00 short cochlear outer hair cells

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

²FDR corrected p-value (Benjamini-Hochberg)