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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod11

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod11 Module size 13 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 51573 GDE1 glycerophosphodiester phosphodiesterase 1 284161 GDPD1 glycerophosphodiester phosphodiesterase domain containing 1 54857 GDPD2 glycerophosphodiester phosphodiesterase domain containing 2 79153 GDPD3 glycerophosphodiester phosphodiesterase domain containing 3 220032 GDPD4 glycerophosphodiester phosphodiesterase domain containing 4 81544 GDPD5 glycerophosphodiester phosphodiesterase domain containing 5 2645 GK glucokinase 2585 GK2 galactokinase 2 256356 GK5 glycerol kinase 5 23729 SHPK sedoheptulokinase 10786 SLC17A3 solute carrier family 17 member 3 6519 SLC3A1 solute carrier family 3 member 1 222642 TSPO2 translocator protein 2

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 3.27e-01 6.89e-12 Reactome Glycerophospholipid catabolism Metabolism 8.65e-02 7.42e-08 GO glycerol 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 2.03e-12 1.39e-09 phosphoric diester hydrolase activity 4.78e-10 2.67e-07 glycerophosphodiester phosphodiesterase activity 4.50e-09 2.16e-06 glycerol kinase activity 2.97e-08 1.25e-05 phosphoric ester hydrolase activity 6.46e-08 3.76e-05 glycerol-3-phosphate biosynthetic process 2.08e-07 1.11e-04 glycerol catabolic process 3.77e-07 1.94e-04 glycerol-3-phosphate metabolic process 2.32e-06 1.03e-03 glycerol metabolic process 4.41e-06 1.84e-03 cellular carbohydrate catabolic process 5.22e-06 1.44e-03 hydrolase activity, acting on ester bonds 1.25e-05 4.73e-03 triglyceride metabolic process 1.67e-05 6.12e-03 alcohol catabolic process 1.81e-05 6.58e-03 carbohydrate metabolic process 2.39e-05 8.40e-03 neutral lipid metabolic process 5.11e-05 1.63e-02 carbohydrate catabolic process 6.39e-05 1.98e-02 glycerolipid metabolic process 3.47e-04 8.30e-02 cellular carbohydrate metabolic process 5.40e-04 8.62e-02 brush border membrane 9.67e-04 1.92e-01 alcohol metabolic process 1.80e-03 2.40e-01 brush border

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 1.14e-02 8.84e-01 TRIGLYCERIDE BIOSYNTHESIS 1.96e-02 1.00e+00 AMINO ACID TRANSPORT ACROSS THE PLASMA MEMBRANE 2.08e-02 1.00e+00 AMINO ACID TRANSPORT ACROSS THE PLASMA MEMBRANE 2.08e-02 1.00e+00 AMINO ACID AND OLIGOPEPTIDE SLC TRANSPORTERS 2.33e-02 1.00e+00 TRIGLYCERIDE BIOSYNTHESIS 3.06e-02 1.00e+00 AMINO ACID AND OLIGOPEPTIDE SLC TRANSPORTERS 3.55e-02 1.00e+00 TRANSPORT OF INORGANIC CATIONS ANIONS AND AMINO ACIDS OLIGOPEPTIDES

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 1.87e-03 1e+00 urinary bladder obstruction 1.87e-03 1e+00 uremia 1.87e-03 1e+00 crystalluria 1.87e-03 1e+00 abnormal circulating creatinine level 1.87e-03 1e+00 urolithiasis 1.88e-03 1e+00 abnormal kidney cortex morphology 3.74e-03 1e+00 abnormal urine amino acid level 3.74e-03 1e+00 ureter obstruction 3.74e-03 1e+00 cystolithiasis 3.75e-03 1e+00 aminoaciduria 7.47e-03 1e+00 kidney cortex atrophy 9.36e-03 1e+00 decreased kidney weight 9.36e-03 1e+00 kidney inflammation 1.50e-02 1e+00 increased circulating creatinine level 1.68e-02 1e+00 abnormal neuronal precursor proliferation 1.86e-02 1e+00 decreased motor neuron number 2.04e-02 1e+00 increased circulating LDL cholesterol level 2.24e-02 1e+00 hydronephrosis 2.40e-02 1e+00 abnormal neuron differentiation 2.43e-02 1e+00 abnormal renal glomerulus morphology

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

²FDR corrected p-value (Benjamini-Hochberg)