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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod30

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod30 Module size 39 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 126133 ALDH16A1 aldehyde dehydrogenase 16 family member A1 217 ALDH2 aldehyde dehydrogenase 2 family member 64577 ALDH8A1 aldehyde dehydrogenase 8 family member A1 30816 ERVW-1 endogenous retrovirus group W member 1, envelope 126917 IFFO2 intermediate filament family orphan 2 5625 PRODH proline dehydrogenase 1 58510 PRODH2 proline dehydrogenase 2 6505 SLC1A1 solute carrier family 1 member 1 6506 SLC1A2 solute carrier family 1 member 2 6507 SLC1A3 solute carrier family 1 member 3 6509 SLC1A4 solute carrier family 1 member 4 6510 SLC1A5 solute carrier family 1 member 5 6511 SLC1A6 solute carrier family 1 member 6 6512 SLC1A7 solute carrier family 1 member 7 206358 SLC36A1 solute carrier family 36 member 1 153201 SLC36A2 solute carrier family 36 member 2 285641 SLC36A3 solute carrier family 36 member 3 120103 SLC36A4 solute carrier family 36 member 4 81539 SLC38A1 solute carrier family 38 member 1 124565 SLC38A10 solute carrier family 38 member 10 151258 SLC38A11 solute carrier family 38 member 11 54407 SLC38A2 solute carrier family 38 member 2 55089 SLC38A4 solute carrier family 38 member 4 92745 SLC38A5 solute carrier family 38 member 5 145389 SLC38A6 solute carrier family 38 member 6 146167 SLC38A8 solute carrier family 38 member 8 153129 SLC38A9 solute carrier family 38 member 9 6523 SLC5A1 solute carrier family 5 member 1 125206 SLC5A10 solute carrier family 5 member 10 115584 SLC5A11 solute carrier family 5 member 11 159963 SLC5A12 solute carrier family 5 member 12 6524 SLC5A2 solute carrier family 5 member 2 6526 SLC5A3 solute carrier family 5 member 3 6527 SLC5A4 solute carrier family 5 member 4 6528 SLC5A5 solute carrier family 5 member 5 8884 SLC5A6 solute carrier family 5 member 6 60482 SLC5A7 solute carrier family 5 member 7 160728 SLC5A8 solute carrier family 5 member 8 200010 SLC5A9 solute carrier family 5 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 4.61e-01 4.03e-14 GO high-affinity glutamate transmembrane transporter activity molecular_function 3.37e-01 1.43e-05 Reactome Proline catabolism Metabolism 3.11e-01 1.43e-05 Reactome Inositol transporters Transport of small molecules 2.99e-01 2.42e-13 GO L-alanine transport biological_process 2.48e-01 4.36e-45 GO amino acid transmembrane transporter activity molecular_function 1.20e-01 4.42e-03 Reactome Metabolism of serotonin Neuronal System 1.07e-01 6.10e-10 Reactome Cellular hexose transport Transport of small molecules 8.46e-02 3.15e-28 GO sodium ion transport biological_process 6.35e-02 4.77e-06 Reactome Proton-coupled neutral amino acid transporters Transport of small molecules 2.52e-02 3.99e-08 Reactome Astrocytic Glutamate-Glutamine Uptake And Metabolism Neuronal System 2.04e-02 3.99e-08 Reactome Neurotransmitter uptake and metabolism In glial cells Neuronal System 1.49e-02 1.03e-26 GO amino acid transmembrane transport biological_process 6.09e-04 2.12e-04 Reactome Organic anion transporters Transport of small molecules 2.38e-05 7.09e-10 GO glycine 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 sodium ion transport 0e+00 0e+00 anion transmembrane transport 0e+00 0e+00 carboxylic acid transmembrane transport 0e+00 0e+00 monovalent inorganic cation transport 0e+00 0e+00 carboxylic acid transport 0e+00 0e+00 metal ion transport 0e+00 0e+00 organic acid transmembrane transport 0e+00 0e+00 anion transport 0e+00 0e+00 amino acid transport 0e+00 0e+00 amino acid transmembrane transport 0e+00 0e+00 organic anion transport 0e+00 0e+00 neutral amino acid transport 0e+00 0e+00 alanine transport 0e+00 0e+00 anion transmembrane transporter activity 0e+00 0e+00 amino acid transmembrane transporter activity 0e+00 0e+00 organic anion transmembrane transporter activity 0e+00 0e+00 carboxylic acid transmembrane transporter activity 0e+00 0e+00 monovalent inorganic cation transmembrane transporter activity 0e+00 0e+00 cation transmembrane transporter activity 0e+00 0e+00 solute:sodium symporter 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 AMINO ACID AND OLIGOPEPTIDE SLC TRANSPORTERS 0.00e+00 0.00e+00 TRANSPORT OF INORGANIC CATIONS ANIONS AND AMINO ACIDS OLIGOPEPTIDES 0.00e+00 0.00e+00 SLC MEDIATED TRANSMEMBRANE TRANSPORT 0.00e+00 0.00e+00 AMINO ACID AND OLIGOPEPTIDE SLC TRANSPORTERS 0.00e+00 0.00e+00 TRANSPORT OF INORGANIC CATIONS ANIONS AND AMINO ACIDS OLIGOPEPTIDES 6.47e-11 2.38e-08 AMINO ACID TRANSPORT ACROSS THE PLASMA MEMBRANE 8.74e-11 2.40e-08 AMINO ACID TRANSPORT ACROSS THE PLASMA MEMBRANE 1.22e-09 3.99e-07 TRANSMISSION ACROSS CHEMICAL SYNAPSES 4.63e-08 1.24e-05 NEURONAL SYSTEM 1.28e-07 3.27e-05 NEUROTRANSMITTER RELEASE CYCLE 2.97e-07 5.52e-05 TRANSMISSION ACROSS CHEMICAL SYNAPSES 4.19e-07 9.98e-05 GLUTAMATE NEUROTRANSMITTER RELEASE CYCLE 2.69e-06 4.37e-04 NEURONAL SYSTEM 2.89e-06 4.67e-04 GLUTAMATE NEUROTRANSMITTER RELEASE CYCLE 4.84e-06 7.62e-04 NEUROTRANSMITTER RELEASE CYCLE 1.36e-04 2.04e-02 TRANSPORT OF GLUCOSE AND OTHER SUGARS BILE SALTS AND ORGANIC ACIDS METAL IONS AND AMINE COMPOUNDS 2.08e-04 2.46e-02 TRANSPORT OF GLUCOSE AND OTHER SUGARS BILE SALTS AND ORGANIC ACIDS METAL IONS AND AMINE COMPOUNDS 3.16e-02 1.00e+00 ETHANOL OXIDATION

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 1.97e-05 7.48e-02 abnormal renal glucose reabsorption 6.87e-05 1.76e-01 optic nerve degeneration 3.00e-04 4.47e-01 increased lactate dehydrogenase level 4.44e-04 5.66e-01 increased urine glucose level 5.07e-04 6.09e-01 abnormal circulating glucose level 6.23e-04 6.88e-01 abnormal urine homeostasis 7.84e-04 7.82e-01 increased cellular sensitivity to hydrogen peroxide 8.12e-04 7.98e-01 decreased retinal ganglion cell number 8.66e-04 8.32e-01 abnormal nerve conduction 1.01e-03 9.05e-01 abnormal response to tactile stimuli 1.49e-03 1.00e+00 increased bone trabecula number 1.60e-03 1.00e+00 abnormal startle reflex 2.08e-03 1.00e+00 decreased circulating amylase level 3.74e-03 1.00e+00 increased urine creatinine level 4.63e-03 1.00e+00 increased circulating aspartate transaminase level 5.87e-03 1.00e+00 increased grip strength 6.21e-03 1.00e+00 increased circulating alanine transaminase level 7.47e-03 1.00e+00 hypoventilation 7.48e-03 1.00e+00 long femur 9.33e-03 1.00e+00 abnormal urine amino acid level

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

²FDR corrected p-value (Benjamini-Hochberg)