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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod353

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod353 Module size 28 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 51166 AADAT aminoadipate aminotransferase 24 ABCA4 ATP binding cassette subfamily A member 4 8540 AGPS alkylglycerone phosphate synthase 150209 AIFM3 apoptosis inducing factor, mitochondria associated 3 55821 ALLC allantoicase 433 ASGR2 asialoglycoprotein receptor 2 388963 C2orf81 chromosome 2 open reading frame 81 883 CCBL1 kynurenine aminotransferase 1 26504 CNNM4 cyclin and CBS domain divalent metal cation transport mediator 4 1371 CPOX coproporphyrinogen oxidase 23584 CTH V-set and immunoglobulin domain containing 2 79758 DHRS12 dehydrogenase/reductase 12 147015 DHRS13 dehydrogenase/reductase 13 207063 DHRSX dehydrogenase/reductase X-linked 84706 GPT2 glutamic--pyruvic transaminase 2 3069 HDLBP high density lipoprotein binding protein 51144 HSD17B12 hydroxysteroid 17-beta dehydrogenase 12 3329 HSPD1 heat shock protein family D (Hsp60) member 1 9361 LONP1 lon peptidase 1, mitochondrial 83752 LONP2 lon peptidase 2, peroxisomal 222236 NAPEPLD N-acyl phosphatidylethanolamine phospholipase D 387129 NPSR1 neuropeptide S receptor 1 54852 PAQR5 progestin and adipoQ receptor family member 5 23517 SKIV2L2 Mtr4 exosome RNA helicase 4891 SLC11A2 solute carrier family 11 member 2 6652 SORD sorbitol dehydrogenase 26019 UPF2 UPF2, regulator of nonsense mediated mRNA decay 65110 UPF3A UPF3A, regulator of nonsense mediated mRNA decay

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 4.31e-01 1.40e-03 Reactome Biosynthesis of A2E, implicated in retinal degradation Signal Transduction#Disease 1.18e-01 2.79e-03 Reactome Cysteine formation from homocysteine Metabolism 1.18e-01 2.79e-03 Reactome Fructose biosynthesis Metabolism 1.18e-01 2.79e-03 Reactome Plasmalogen biosynthesis Metabolism 4.26e-02 6.70e-05 GO protein quality control for misfolded or incompletely synthesized proteins 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 1.25e-05 3.20e-03 cofactor binding 2.88e-05 6.88e-03 ATP-dependent peptidase activity 7.28e-05 1.49e-02 peroxisomal matrix 8.24e-05 1.75e-02 oxidoreductase activity 1.73e-04 3.33e-02 pyridoxal phosphate binding 3.29e-04 7.94e-02 2-oxoglutarate metabolic process 3.54e-04 8.45e-02 response to inorganic substance 4.05e-04 6.73e-02 exon-exon junction complex 5.51e-04 1.21e-01 heme biosynthetic process 7.41e-04 1.55e-01 response to metal ion 7.54e-04 1.20e-01 transaminase activity 9.56e-04 1.90e-01 carboxylic acid catabolic process 1.06e-03 2.07e-01 porphyrin-containing compound biosynthetic process 1.07e-03 2.08e-01 heme metabolic process 1.24e-03 2.35e-01 misfolded or incompletely synthesized protein catabolic process 1.37e-03 2.55e-01 response to iron ion 1.38e-03 1.92e-01 peroxisome 1.45e-03 2.67e-01 cellular amino acid catabolic process 1.52e-03 2.08e-01 mitochondrial membrane 1.58e-03 2.29e-01 telomeric DNA binding

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 3.93e-04 4.38e-02 NONSENSE MEDIATED DECAY ENHANCED BY THE EXON JUNCTION COMPLEX 6.43e-04 6.77e-02 TRYPTOPHAN CATABOLISM 6.48e-04 6.82e-02 AMINO ACID SYNTHESIS AND INTERCONVERSION TRANSAMINATION 1.54e-03 1.71e-01 NONSENSE MEDIATED DECAY ENHANCED BY THE EXON JUNCTION COMPLEX 1.70e-03 1.86e-01 TRYPTOPHAN CATABOLISM 1.84e-03 1.98e-01 METABOLISM OF AMINO ACIDS AND DERIVATIVES 1.88e-03 2.02e-01 AMINO ACID SYNTHESIS AND INTERCONVERSION TRANSAMINATION 2.35e-03 2.15e-01 METABOLISM OF AMINO ACIDS AND DERIVATIVES 6.31e-03 5.53e-01 METABOLISM OF MRNA 6.63e-03 5.24e-01 METABOLISM OF MRNA 1.02e-02 8.13e-01 METABOLISM OF RNA 1.28e-02 8.97e-01 METABOLISM OF RNA 2.72e-02 1.00e+00 SYNTHESIS OF VERY LONG CHAIN FATTY ACYL COAS 3.18e-02 1.00e+00 SYNTHESIS OF VERY LONG CHAIN FATTY ACYL COAS 3.38e-02 1.00e+00 FATTY ACYL COA BIOSYNTHESIS 3.81e-02 1.00e+00 FATTY ACYL COA BIOSYNTHESIS 4.80e-02 1.00e+00 TRIGLYCERIDE BIOSYNTHESIS 4.86e-02 1.00e+00 PEROXISOMAL LIPID METABOLISM

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 1.58e-04 3.05e-01 abnormal lens morphology 2.49e-04 3.98e-01 partial embryonic lethality between implantation and placentation 8.00e-04 7.91e-01 cataract 1.68e-03 1.00e+00 abnormal lens fiber morphology 2.26e-03 1.00e+00 increased sensitivity to induced morbidity/mortality 3.74e-03 1.00e+00 high mean erythrocyte cell number 5.61e-03 1.00e+00 decreased urine magnesium level 5.61e-03 1.00e+00 abnormal pluripotent precursor cell morphology/development 5.61e-03 1.00e+00 hemolysis 5.61e-03 1.00e+00 increased erythrocyte protoporphyrin level 5.61e-03 1.00e+00 increased erythrocyte clearance 7.47e-03 1.00e+00 hydropic eye lens fibers 7.48e-03 1.00e+00 abnormal tooth mineralization 7.48e-03 1.00e+00 abnormal Bruch membrane morphology 9.34e-03 1.00e+00 decreased lactate dehydrogenase level 9.34e-03 1.00e+00 abnormal epidermal pigmentation 9.43e-03 1.00e+00 decreased cellular hemoglobin content 1.12e-02 1.00e+00 early eyelid opening 1.12e-02 1.00e+00 microcytic anemia 1.27e-02 1.00e+00 abnormal vitamin A level

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

²FDR corrected p-value (Benjamini-Hochberg)