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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod312

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod312 Module size 39 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 79850 FAM57A family with sequence similarity 57 member A 27165 GLS2 glutaminase 2 64747 MFSD1 major facilitator superfamily domain containing 1 6557 SLC12A1 solute carrier family 12 member 1 6558 SLC12A2 solute carrier family 12 member 2 6559 SLC12A3 solute carrier family 12 member 3 6560 SLC12A4 solute carrier family 12 member 4 57468 SLC12A5 solute carrier family 12 member 5 9990 SLC12A6 solute carrier family 12 member 6 10723 SLC12A7 solute carrier family 12 member 7 84561 SLC12A8 solute carrier family 12 member 8 56996 SLC12A9 solute carrier family 12 member 9 117247 SLC16A10 solute carrier family 16 member 10 162515 SLC16A11 solute carrier family 16 member 11 387700 SLC16A12 solute carrier family 16 member 12 9121 SLC16A5 solute carrier family 16 member 5 9120 SLC16A6 solute carrier family 16 member 6 220963 SLC16A9 solute carrier family 16 member 9 387775 SLC22A10 solute carrier family 22 member 10 55867 SLC22A11 solute carrier family 22 member 11 116085 SLC22A12 solute carrier family 22 member 12 283238 SLC22A24 solute carrier family 22 member 24 387601 SLC22A25 solute carrier family 22 member 25 9376 SLC22A8 solute carrier family 22 member 8 114571 SLC22A9 solute carrier family 22 member 9 6520 SLC3A2 solute carrier family 3 member 2 6541 SLC7A1 solute carrier family 7 member 1 56301 SLC7A10 solute carrier family 7 member 10 23657 SLC7A11 solute carrier family 7 member 11 157724 SLC7A13 solute carrier family 7 member 13 57709 SLC7A14 solute carrier family 7 member 14 6542 SLC7A2 solute carrier family 7 member 2 84889 SLC7A3 solute carrier family 7 member 3 6545 SLC7A4 solute carrier family 7 member 4 8140 SLC7A5 solute carrier family 7 member 5 9057 SLC7A6 solute carrier family 7 member 6 9056 SLC7A7 solute carrier family 7 member 7 23428 SLC7A8 solute carrier family 7 member 8 11136 SLC7A9 solute carrier family 7 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 6.79e-01 3.48e-25 GO potassium:chloride symporter activity molecular_function 2.61e-01 9.17e-08 Reactome Organic anion transport Transport of small molecules 2.23e-01 1.31e-18 GO L-amino acid transmembrane transporter activity molecular_function 2.21e-01 3.22e-13 GO monocarboxylic acid transport biological_process 1.49e-01 4.66e-25 Reactome Amino acid transport across the plasma membrane Transport of small molecules 1.13e-01 1.18e-19 Reactome Cation-coupled Chloride cotransporters Transport of small molecules 6.59e-02 7.59e-13 GO inorganic anion transport biological_process 5.81e-02 2.17e-16 Reactome Basigin interactions Hemostasis 4.79e-02 3.20e-07 GO basic amino acid transmembrane transporter activity molecular_function 4.34e-02 1.09e-06 GO urate metabolic process biological_process 3.73e-02 3.82e-13 GO cellular amino acid metabolic process 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 anion transmembrane transport 0e+00 0e+00 chloride transmembrane transport 0e+00 0e+00 anion transport 0e+00 0e+00 chloride transport 0e+00 0e+00 amino acid transport 0e+00 0e+00 carboxylic acid transport 0e+00 0e+00 organic anion transport 0e+00 0e+00 organic acid transmembrane transport 0e+00 0e+00 sodium-independent organic anion transport 0e+00 0e+00 L-alpha-amino acid transmembrane transport 0e+00 0e+00 carboxylic acid transmembrane transport 0e+00 0e+00 amino acid transmembrane transport 0e+00 0e+00 cation:chloride symporter activity 0e+00 0e+00 anion transmembrane transporter activity 0e+00 0e+00 cation transmembrane transporter activity 0e+00 0e+00 symporter activity 0e+00 0e+00 secondary active transmembrane transporter activity 0e+00 0e+00 antiporter activity 0e+00 0e+00 amino acid transmembrane transporter activity

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 0.00e+00 0.00e+00 TRANSMEMBRANE TRANSPORT OF SMALL MOLECULES 0.00e+00 0.00e+00 SLC MEDIATED TRANSMEMBRANE TRANSPORT 0.00e+00 0.00e+00 TRANSPORT OF INORGANIC CATIONS ANIONS AND AMINO ACIDS OLIGOPEPTIDES 0.00e+00 0.00e+00 BASIGIN INTERACTIONS 0.00e+00 0.00e+00 AMINO ACID TRANSPORT ACROSS THE PLASMA MEMBRANE 0.00e+00 0.00e+00 AMINO ACID AND OLIGOPEPTIDE SLC TRANSPORTERS 0.00e+00 0.00e+00 SLC MEDIATED TRANSMEMBRANE TRANSPORT 0.00e+00 0.00e+00 TRANSPORT OF INORGANIC CATIONS ANIONS AND AMINO ACIDS OLIGOPEPTIDES 0.00e+00 0.00e+00 BASIGIN INTERACTIONS 0.00e+00 0.00e+00 AMINO ACID TRANSPORT ACROSS THE PLASMA MEMBRANE 0.00e+00 0.00e+00 AMINO ACID AND OLIGOPEPTIDE SLC TRANSPORTERS 3.61e-11 1.35e-08 CELL SURFACE INTERACTIONS AT THE VASCULAR WALL 1.43e-09 3.42e-07 CELL SURFACE INTERACTIONS AT THE VASCULAR WALL 6.09e-06 9.43e-04 ORGANIC CATION ANION ZWITTERION TRANSPORT 2.36e-05 4.20e-03 ORGANIC CATION ANION ZWITTERION TRANSPORT 8.25e-03 6.28e-01 TRANSPORT OF GLUCOSE AND OTHER SUGARS BILE SALTS AND ORGANIC ACIDS METAL IONS AND AMINE COMPOUNDS 9.53e-03 7.72e-01 TRANSPORT OF GLUCOSE AND OTHER SUGARS BILE SALTS AND ORGANIC ACIDS METAL IONS AND AMINE COMPOUNDS 3.84e-02 1.00e+00 GLUTAMATE NEUROTRANSMITTER RELEASE CYCLE

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 1.18e-05 5.28e-02 aminoaciduria 1.33e-04 2.74e-01 increased urine creatinine level 2.71e-04 4.22e-01 decreased urine uric acid level 2.91e-04 4.41e-01 abnormal circulating amino acid level 6.80e-04 7.25e-01 akinesia 1.07e-03 9.34e-01 increased urine pH 1.22e-03 1.00e+00 decreased urine sodium level 1.87e-03 1.00e+00 abnormal renal sodium ion transport 2.19e-03 1.00e+00 deafness 2.34e-03 1.00e+00 abnormal amino acid level 4.25e-03 1.00e+00 decreased systemic arterial blood pressure 7.03e-03 1.00e+00 tonic-clonic seizures 7.46e-03 1.00e+00 abnormal renal tubule morphology 7.48e-03 1.00e+00 decreased total retina thickness 7.51e-03 1.00e+00 alkalosis 7.51e-03 1.00e+00 abnormal summary potential 9.33e-03 1.00e+00 increased urinary bladder weight 9.37e-03 1.00e+00 increased urine osmolality 1.04e-02 1.00e+00 ataxia 1.12e-02 1.00e+00 abnormal abdominal wall morphology

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

²FDR corrected p-value (Benjamini-Hochberg)