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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod62

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod62 Module size 18 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 6529 SLC6A1 solute carrier family 6 member 1 6538 SLC6A11 solute carrier family 6 member 11 6539 SLC6A12 solute carrier family 6 member 12 6540 SLC6A13 solute carrier family 6 member 13 11254 SLC6A14 solute carrier family 6 member 14 55117 SLC6A15 solute carrier family 6 member 15 388662 SLC6A17 solute carrier family 6 member 17 348932 SLC6A18 solute carrier family 6 member 18 340024 SLC6A19 solute carrier family 6 member 19 6530 SLC6A2 solute carrier family 6 member 2 54716 SLC6A20 solute carrier family 6 member 20 6532 SLC6A4 solute carrier family 6 member 4 9152 SLC6A5 solute carrier family 6 member 5 6533 SLC6A6 solute carrier family 6 member 6 6534 SLC6A7 solute carrier family 6 member 7 6535 SLC6A8 solute carrier family 6 member 8 6536 SLC6A9 solute carrier family 6 member 9 57393 TMEM27 collectrin, amino acid transport regulator

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 4.02e-01 4.70e-30 GO neurotransmitter:sodium symporter activity molecular_function 3.84e-01 8.44e-13 Reactome Reuptake of GABA Neuronal System 3.08e-01 1.60e-41 Reactome Na+/Cl- dependent neurotransmitter transporters Transport of small molecules 2.85e-02 3.14e-03 Reactome Serotonin clearance from the synaptic cleft Neuronal System

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 neurotransmitter transport 0e+00 0e+00 anion transmembrane transport 0e+00 0e+00 carboxylic acid transmembrane transport 0e+00 0e+00 carboxylic acid transport 0e+00 0e+00 neutral amino acid 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 monovalent inorganic cation transmembrane transporter activity 0e+00 0e+00 cation transmembrane transporter activity 0e+00 0e+00 solute:sodium symporter activity 0e+00 0e+00 symporter activity 0e+00 0e+00 amino acid transmembrane transporter activity 0e+00 0e+00 metal ion transmembrane transporter activity 0e+00 0e+00 secondary active transmembrane transporter activity 0e+00 0e+00 sodium ion transmembrane transporter activity 0e+00 0e+00 organic anion transmembrane transporter activity 0e+00 0e+00 carboxylic 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 NA CL DEPENDENT NEUROTRANSMITTER TRANSPORTERS 0.00e+00 0.00e+00 SLC MEDIATED TRANSMEMBRANE TRANSPORT 0.00e+00 0.00e+00 AMINE COMPOUND SLC TRANSPORTERS 0.00e+00 0.00e+00 TRANSPORT OF GLUCOSE AND OTHER SUGARS BILE SALTS AND ORGANIC ACIDS METAL IONS AND AMINE COMPOUNDS 0.00e+00 0.00e+00 NA CL DEPENDENT NEUROTRANSMITTER TRANSPORTERS 0.00e+00 0.00e+00 SLC MEDIATED TRANSMEMBRANE TRANSPORT 0.00e+00 0.00e+00 AMINE COMPOUND SLC TRANSPORTERS 0.00e+00 0.00e+00 TRANSPORT OF GLUCOSE AND OTHER SUGARS BILE SALTS AND ORGANIC ACIDS METAL IONS AND AMINE COMPOUNDS 1.04e-10 2.84e-08 AMINO ACID TRANSPORT ACROSS THE PLASMA MEMBRANE 2.51e-10 8.78e-08 AMINO ACID TRANSPORT ACROSS THE PLASMA MEMBRANE 1.99e-09 4.67e-07 AMINO ACID AND OLIGOPEPTIDE SLC TRANSPORTERS 2.61e-09 8.11e-07 AMINO ACID AND OLIGOPEPTIDE SLC TRANSPORTERS 3.75e-09 1.14e-06 TRANSPORT OF INORGANIC CATIONS ANIONS AND AMINO ACIDS OLIGOPEPTIDES 4.10e-09 9.35e-07 TRANSPORT OF INORGANIC CATIONS ANIONS AND AMINO ACIDS OLIGOPEPTIDES 1.80e-05 3.28e-03 GABA SYNTHESIS RELEASE REUPTAKE AND DEGRADATION 2.80e-04 3.86e-02 NEUROTRANSMITTER RELEASE CYCLE 2.90e-04 3.33e-02 GABA SYNTHESIS RELEASE REUPTAKE AND DEGRADATION 2.61e-03 2.35e-01 NEUROTRANSMITTER RELEASE CYCLE 1.23e-02 9.39e-01 TRANSMISSION ACROSS CHEMICAL SYNAPSES

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 2.42e-07 2.87e-03 abnormal renal transport 2.88e-06 1.97e-02 aminoaciduria 1.09e-04 2.40e-01 abnormal amino acid level 1.43e-04 2.88e-01 abnormal inhibitory postsynaptic currents 1.27e-03 1.00e+00 behavioral despair 1.33e-03 1.00e+00 hyperactivity 1.78e-03 1.00e+00 hypoactivity 1.97e-03 1.00e+00 dilated cardiomyopathy 2.18e-03 1.00e+00 impaired behavioral response to xenobiotic 3.76e-03 1.00e+00 abnormal response to novel object 5.61e-03 1.00e+00 hyperactivity elicited by ethanol administration 5.61e-03 1.00e+00 abnormal bitter taste sensitivity 7.33e-03 1.00e+00 decreased cardiac muscle contractility 7.47e-03 1.00e+00 decreased circulating carnitine level 7.47e-03 1.00e+00 abnormal short term object recognition memory 7.47e-03 1.00e+00 abnormal sleep behavior 7.53e-03 1.00e+00 abnormal neuron physiology 7.67e-03 1.00e+00 complete preweaning lethality 9.33e-03 1.00e+00 increased right ventricle systolic pressure 9.33e-03 1.00e+00 decreased creatine level

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

²FDR corrected p-value (Benjamini-Hochberg)