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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod186

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod186 Module size 21 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 84226 C2orf16 chromosome 2 open reading frame 16 1400 CRMP1 collapsin response mediator protein 1 51706 CYB5R1 cytochrome b5 reductase 1 51700 CYB5R2 cytochrome b5 reductase 2 1727 CYB5R3 cytochrome b5 reductase 3 51167 CYB5R4 cytochrome b5 reductase 4 606495 CYB5RL cytochrome b5 reductase like 1723 DHODH dihydroorotate dehydrogenase (quinone) 1806 DPYD dihydropyrimidine dehydrogenase 1807 DPYS dihydropyrimidinase 1808 DPYSL2 dihydropyrimidinase like 2 1809 DPYSL3 dihydropyrimidinase like 3 10570 DPYSL4 dihydropyrimidinase like 4 56896 DPYSL5 dihydropyrimidinase like 5 2232 FDXR ferredoxin reductase 83943 IMMP2L inner mitochondrial membrane peptidase subunit 2 92106 OXNAD1 oxidoreductase NAD binding domain containing 1 9963 SLC23A1 solute carrier family 23 member 1 9962 SLC23A2 solute carrier family 23 member 2 151295 SLC23A3 solute carrier family 23 member 3 7372 UMPS uridine monophosphate synthetase

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 3.26e-01 3.48e-06 Reactome Pyrimidine biosynthesis Metabolism 2.76e-01 1.16e-06 GO L-ascorbic acid transmembrane transporter activity molecular_function 2.75e-01 1.16e-06 GO L-ascorbic acid transmembrane transport biological_process 1.55e-01 4.05e-12 Reactome CRMPs in Sema3A signaling Developmental Biology 8.63e-02 5.26e-10 Reactome Erythrocytes take up carbon dioxide and release oxygen Transport of small molecules 8.57e-02 5.26e-10 Reactome O2/CO2 exchange in erythrocytes Transport of small molecules 4.67e-02 6.40e-08 Reactome Vitamin C (ascorbate) metabolism Metabolism 4.45e-02 3.26e-07 GO filamin binding molecular_function 2.83e-02 3.32e-03 Reactome Electron transport from NADPH to Ferredoxin Metabolism 2.15e-02 6.34e-05 GO pyrimidine nucleoside catabolic 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 8.10e-13 5.61e-10 cytochrome-b5 reductase activity, acting on NAD(P)H 2.45e-12 1.68e-09 oxidoreductase activity, acting on NAD(P)H, heme protein as acceptor 1.94e-08 1.22e-05 pyrimidine nucleobase metabolic process 3.16e-08 1.32e-05 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds 1.19e-07 4.51e-05 filamin binding 1.83e-07 6.71e-05 oxidoreductase activity, acting on NAD(P)H 2.23e-07 8.05e-05 oxidoreductase activity 4.68e-07 2.36e-04 bicarbonate transport 1.67e-06 7.61e-04 L-ascorbic acid metabolic process 4.99e-06 2.06e-03 pyrimidine nucleoside metabolic process 1.52e-05 5.63e-03 organic anion transport 1.91e-05 6.90e-03 uracil metabolic process 1.91e-05 6.90e-03 'de novo' UMP biosynthetic process 2.39e-05 8.40e-03 'de novo' pyrimidine nucleobase biosynthetic process 2.85e-05 6.81e-03 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides 2.90e-05 9.97e-03 sterol metabolic process 2.98e-05 1.02e-02 thymine metabolic process 2.98e-05 1.02e-02 thymine catabolic process 2.98e-05 1.02e-02 pyrimidine nucleobase catabolic process 3.39e-05 1.14e-02 steroid biosynthetic process

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 3.06e-11 1.15e-08 CRMPS IN SEMA3A SIGNALING 1.06e-10 2.89e-08 CRMPS IN SEMA3A SIGNALING 8.30e-09 2.46e-06 SEMAPHORIN INTERACTIONS 7.37e-08 1.46e-05 SEMAPHORIN INTERACTIONS 2.41e-07 5.94e-05 PYRIMIDINE METABOLISM 3.33e-07 6.15e-05 PYRIMIDINE METABOLISM 9.21e-06 1.77e-03 AXON GUIDANCE 2.87e-05 5.05e-03 METABOLISM OF NUCLEOTIDES 4.18e-05 5.68e-03 AXON GUIDANCE 5.41e-05 7.24e-03 METABOLISM OF NUCLEOTIDES 1.05e-04 1.62e-02 METABOLISM OF VITAMINS AND COFACTORS 1.34e-04 2.02e-02 DEVELOPMENTAL BIOLOGY 3.15e-04 4.29e-02 PYRIMIDINE CATABOLISM 6.71e-04 7.04e-02 METABOLISM OF VITAMINS AND COFACTORS 8.49e-04 8.68e-02 PYRIMIDINE CATABOLISM 1.85e-02 1.00e+00 RECYCLING PATHWAY OF L1 2.21e-02 1.00e+00 RECYCLING PATHWAY OF L1

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 1.96e-05 7.47e-02 abnormal vitamin C level 3.30e-04 4.74e-01 abnormal hippocampus pyramidal cell morphology 1.87e-03 1.00e+00 abnormal adrenocortical cell morphology 1.87e-03 1.00e+00 abnormal gland physiology 5.32e-03 1.00e+00 abnormal dopamine level 5.61e-03 1.00e+00 abnormal penile erection 5.61e-03 1.00e+00 abnormal vitamin absorption 5.62e-03 1.00e+00 hyperlipidemia 7.47e-03 1.00e+00 abnormal renal filtration rate 9.36e-03 1.00e+00 impaired synaptic plasticity 9.36e-03 1.00e+00 decreased circulating corticosterone level 1.09e-02 1.00e+00 abnormal Purkinje cell dendrite morphology 1.12e-02 1.00e+00 absent long term depression 1.12e-02 1.00e+00 decreased pancreatic beta cell number 1.12e-02 1.00e+00 abnormal adrenal gland secretion 1.30e-02 1.00e+00 abnormal adrenaline level 1.31e-02 1.00e+00 abnormal hippocampus CA1 region morphology 1.68e-02 1.00e+00 abnormal hippocampus pyramidal cell layer 2.23e-02 1.00e+00 absent mature ovarian follicles 2.41e-02 1.00e+00 aminoaciduria

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

²FDR corrected p-value (Benjamini-Hochberg)