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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod374

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod374 Module size 82 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 22 ABCB7 ATP binding cassette subfamily B member 7 84945 ABHD13 abhydrolase domain containing 13 79777 ACBD4 acyl-CoA binding domain containing 4 641371 ACOT1 acyl-CoA thioesterase 1 56 ACRV1 acrosomal vesicle protein 1 57037 ANKMY2 ankyrin repeat and MYND domain containing 2 327 APEH acylaminoacyl-peptide hydrolase 51062 ATL1 atlastin GTPase 1 475 ATOX1 antioxidant 1 copper chaperone 9689 BZW1 basic leucine zipper and W2 domains 1 28969 BZW2 basic leucine zipper and W2 domains 2 10902 C11orf58 bromodomain containing 8 30850 CDR2L cerebellar degeneration related protein 2 like 1185 CLCN6 chloride voltage-gated channel 6 1186 CLCN7 chloride voltage-gated channel 7 292696 CLPTM1 CLPTM1, transmembrane protein 1521 CTSW cathepsin W 50626 CYHR1 cysteine and histidine rich 1 65992 DDRGK1 DDRGK domain containing 1 1777 DNASE2 deoxyribonuclease 2, lysosomal 1800 DPEP1 dipeptidase 1 30844 EHD4 EH domain containing 4 51104 FAM108B1 abhydrolase domain containing 17B 58489 FAM108C1 abhydrolase domain containing 17C 2644 GCHFR GTP cyclohydrolase I feedback regulator 78997 GDAP1L1 ganglioside induced differentiation associated protein 1 like 1 51527 GSKIP GSK3B interacting protein 25994 HIGD1A HIG1 hypoxia inducible domain family member 1A 26353 HSPB8 heat shock protein family B (small) member 8 3476 IGBP1 immunoglobulin binding protein 1 51015 ISOC1 isochorismatase domain containing 1 79763 ISOC2 isochorismatase domain containing 2 51133 KCTD3 potassium channel tetramerization domain containing 3 80856 KIAA1715 lunapark, ER junction formation factor 646262 LACTBL1 lactamase beta like 1 8270 LAGE3 L antigen family member 3 55788 LMBRD1 LMBR1 domain containing 1 91694 LONRF1 LON peptidase N-terminal domain and ring finger 1 254013 METTL20 electron transfer flavoprotein subunit beta lysine methyltransferase 221143 N6AMT2 EEF1A lysine methyltransferase 1 79400 NOX5 NADPH oxidase 5 10101 NUBP1 nucleotide binding protein 2 10101 NUBP2 nucleotide binding protein 2 80224 NUBPL nucleotide binding protein like 11054 OGFR opioid growth factor receptor 80025 PANK2 pantothenate kinase 2 55486 PARL presenilin associated rhomboid like 56965 PARP6 poly(ADP-ribose) polymerase family member 6 5092 PCBD1 pterin-4 alpha-carbinolamine dehydratase 1 84105 PCBD2 pterin-4 alpha-carbinolamine dehydratase 2 5110 PCMT1 protein-L-isoaspartate (D-aspartate) O-methyltransferase 23612 PHLDA3 pleckstrin homology like domain family A member 3 10226 PLIN3 perilipin 3 51400 PPME1 protein phosphatase methylesterase 1 84722 PSRC1 proline and serine rich coiled-coil 1 5763 PTMS parathymosin 5805 PTS 6-pyruvoyltetrahydropterin synthase 54439 RBM27 RNA binding motif protein 27 84236 RHBDD1 rhomboid domain containing 1 25807 RHBDD3 rhomboid domain containing 3 6433 SFSWAP splicing factor SWAP 6451 SH3BGRL SH3 domain binding glutamate rich protein like 153769 SH3RF2 SH3 domain containing ring finger 2 92799 SHKBP1 SH3KBP1 binding protein 1 81034 SLC25A32 solute carrier family 25 member 32 10879 SMR3B submaxillary gland androgen regulated protein 3B 6697 SPR sepiapterin reductase 256979 SUN3 Sad1 and UNC84 domain containing 3 619345 SURF2 surfeit 2 26099 SZRD1 SUZ RNA binding domain containing 1 25937 TAZ WW domain containing transcription regulator 1 100302736 TMED7-TICAM2 TMED7-TICAM2 readthrough 161145 TMEM229B transmembrane protein 229B 26092 TOR1AIP1 torsin 1A interacting protein 1 27433 TOR2A torsin family 2 member A 6738 TROVE2 TROVE domain family member 2 129450 TYW5 tRNA-yW synthesizing protein 5 50613 UBQLN3 ubiquilin 3 55148 UBR7 ubiquitin protein ligase E3 component n-recognin 7 (putative) 10869 USP19 ubiquitin specific peptidase 19 56270 WDR45L WD repeat domain 45B 23038 WDTC1 WD and tetratricopeptide repeats 1

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 3.37e-01 6.08e-09 GO tetrahydrobiopterin biosynthetic process biological_process 4.37e-02 3.23e-05 GO iron-sulfur cluster assembly biological_process 2.88e-02 5.81e-06 GO cofactor metabolic process biological_process 1.77e-02 7.36e-04 GO antiporter activity molecular_function 4.98e-03 8.81e-04 GO voltage-gated chloride channel activity molecular_function

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 1.56e-08 9.91e-06 tetrahydrobiopterin biosynthetic process 6.66e-08 3.87e-05 pteridine-containing compound metabolic process 2.15e-07 1.15e-04 pteridine-containing compound biosynthetic process 4.31e-06 1.81e-03 cofactor metabolic process 1.81e-05 6.58e-03 coenzyme biosynthetic process 3.00e-05 1.03e-02 protein homooligomerization 5.76e-05 1.81e-02 protein oligomerization 6.68e-05 2.06e-02 regulation of nitric-oxide synthase activity 1.12e-04 2.29e-02 phenylalanine 4-monooxygenase activity 2.88e-04 7.11e-02 nitric oxide biosynthetic process 2.94e-04 7.23e-02 nitric oxide metabolic process 3.88e-04 9.10e-02 regulation of oxidoreductase activity 5.62e-04 1.23e-01 mitochondrion morphogenesis 6.19e-04 1.33e-01 regulation of proteolysis 7.85e-04 1.62e-01 negative regulation of protein kinase B signaling 9.68e-04 1.49e-01 4 iron, 4 sulfur cluster binding 1.13e-03 1.62e-01 organelle inner membrane 1.17e-03 2.24e-01 reactive oxygen species biosynthetic process 1.23e-03 1.84e-01 voltage-gated chloride channel activity 1.31e-03 1.95e-01 cadherin binding

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 2.71e-07 5.06e-05 TETRAHYDROBIOPTERIN BH4 SYNTHESIS RECYCLING SALVAGE AND REGULATION 3.01e-07 7.32e-05 TETRAHYDROBIOPTERIN BH4 SYNTHESIS RECYCLING SALVAGE AND REGULATION 1.57e-06 3.43e-04 ENOS ACTIVATION AND REGULATION 2.06e-06 3.42e-04 ENOS ACTIVATION AND REGULATION 5.02e-03 4.12e-01 LYSOSOME VESICLE BIOGENESIS 5.33e-03 4.82e-01 METABOLISM OF VITAMINS AND COFACTORS 8.38e-03 6.35e-01 METABOLISM OF VITAMINS AND COFACTORS 9.67e-03 7.80e-01 LYSOSOME VESICLE BIOGENESIS 3.28e-02 1.00e+00 VITAMIN B5 PANTOTHENATE METABOLISM 3.53e-02 1.00e+00 VITAMIN B5 PANTOTHENATE METABOLISM

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 1.79e-05 7.02e-02 abnormal neopterin level 2.58e-04 4.08e-01 lysosomal protein accumulation 2.91e-04 4.41e-01 abnormal amino acid level 2.15e-03 1.00e+00 abnormal serotonin level 2.27e-03 1.00e+00 abnormal noradrenaline level 2.35e-03 1.00e+00 hypopigmentation 2.38e-03 1.00e+00 decreased dopamine level 3.77e-03 1.00e+00 neurodegeneration 4.49e-03 1.00e+00 decreased skeletal muscle fiber diameter 5.62e-03 1.00e+00 absent photoreceptor inner segment 5.63e-03 1.00e+00 abnormal tooth eruption 5.65e-03 1.00e+00 optic nerve atrophy 7.25e-03 1.00e+00 abnormal autophagy 7.50e-03 1.00e+00 no swallowing reflex 9.04e-03 1.00e+00 decreased susceptibility to induced muscular atrophy 9.09e-03 1.00e+00 abnormal cardiac cell glucose uptake 9.35e-03 1.00e+00 abnormal copper homeostasis 9.35e-03 1.00e+00 decreased liver copper level 1.08e-02 1.00e+00 tremors 1.12e-02 1.00e+00 accumulation of giant lysosomes in kidney/renal tubule cells

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

²FDR corrected p-value (Benjamini-Hochberg)