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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod303

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod303 Module size 76 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 91452 ACBD5 acyl-CoA binding domain containing 5 134637 ADAT2 adenosine deaminase, tRNA specific 2 113179 ADAT3 adenosine deaminase, tRNA specific 3 84266 ALKBH7 alkB homolog 7 83858 ATAD3B ATPase family, AAA domain containing 3B 79946 C10orf95 chromosome 10 open reading frame 95 91574 C12orf65 chromosome 12 open reading frame 65 79020 C7orf25 chromosome 7 open reading frame 25 51654 CDK5RAP1 CDK5 regulatory subunit associated protein 1 285521 COX18 cytochrome c oxidase assembly factor COX18 92675 DTD1 D-tyrosyl-tRNA deacylase 1 60678 EEFSEC eukaryotic elongation factor, selenocysteine-tRNA specific 440275 EIF2AK4 eukaryotic translation initiation factor 2 alpha kinase 4 1967 EIF2B1 eukaryotic translation initiation factor 2B subunit alpha 8892 EIF2B2 eukaryotic translation initiation factor 2B subunit beta 8891 EIF2B3 eukaryotic translation initiation factor 2B subunit gamma 8890 EIF2B4 eukaryotic translation initiation factor 2B subunit delta 8893 EIF2B5 eukaryotic translation initiation factor 2B subunit epsilon 146705 ENTHD2 TEPSIN, adaptor related protein complex 4 accessory protein 26284 ERAL1 Era like 12S mitochondrial rRNA chaperone 1 79152 FAAH fatty acid 2-hydroxylase 158584 FAAH2 fatty acid amide hydrolase 2 196483 FAM86A eukaryotic elongation factor 2 lysine methyltransferase 91893 FDXACB1 ferredoxin-fold anticodon binding domain containing 1 2235 FECH ferrochelatase 283459 GATC glutamyl-tRNA amidotransferase subunit C 10985 GCN1L1 GCN1, eIF2 alpha kinase activator homolog 29083 GTPBP8 GTP binding protein 8 (putative) 3145 HMBS hydroxymethylbilane synthase 729920 ISPD isoprenoid synthase domain containing 144811 LACC1 laccase domain containing 1 115353 LRRC42 leucine rich repeat containing 42 51360 MBTPS2 membrane bound transcription factor peptidase, site 2 196074 METTL15 methyltransferase like 15 79066 METTL16 methyltransferase like 16 9617 MTRF1 mitochondrial translation release factor 1 54516 MTRF1L mitochondrial translational release factor 1 like 29104 N6AMT1 N-6 adenine-specific DNA methyltransferase 1 9397 NMT2 N-myristoyltransferase 2 53343 NUDT10 nudix hydrolase 9 55190 NUDT11 nudix hydrolase 11 29789 OLA1 Obg like ATPase 1 55644 OSGEP O-sialoglycoprotein endopeptidase 64172 OSGEPL1 O-sialoglycoprotein endopeptidase like 1 115294 PCMTD1 protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 1 55251 PCMTD2 protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 2 27166 PRELID1 PRELI domain containing 1 11212 PROSC pyridoxal phosphate binding protein 5631 PRPS1 phosphoribosyl pyrophosphate synthetase 1 221823 PRPS1L1 phosphoribosyl pyrophosphate synthetase 1-like 1 5634 PRPS2 phosphoribosyl pyrophosphate synthetase 2 5635 PRPSAP1 phosphoribosyl pyrophosphate synthetase associated protein 1 5636 PRPSAP2 phosphoribosyl pyrophosphate synthetase associated protein 2 118672 PSTK phosphoseryl-tRNA kinase 55278 QRSL1 QRSL1, glutaminyl-tRNA amidotransferase subunit A 81890 QTRT1 queuine tRNA-ribosyltransferase catalytic subunit 1 79691 QTRTD1 queuine tRNA-ribosyltransferase accessory subunit 2 343035 RD3 retinal degeneration 3, GUCY2D regulator 55312 RFK riboflavin kinase 57414 RHBDD2 rhomboid domain containing 2 113000 RPUSD1 RNA pseudouridylate synthase domain containing 1 27079 RPUSD2 RNA pseudouridylate synthase domain containing 2 285367 RPUSD3 RNA pseudouridylate synthase domain containing 3 84881 RPUSD4 RNA pseudouridylate synthase domain containing 4 94097 SFXN5 sideroflexin 5 401612 SLC25A53 solute carrier family 25 member 53 10650 SLMO1 PRELI domain containing 3A 51012 SLMO2 PRELI domain containing 3B 6676 SPAG4 sperm associated antigen 4 137695 TMEM68 transmembrane protein 68 54802 TRIT1 tRNA isopentenyltransferase 1 55687 TRMU tRNA 5-methylaminomethyl-2-thiouridylate methyltransferase 200081 TXLNA taxilin alpha 7389 UROD uroporphyrinogen decarboxylase 22846 VASH1 vasohibin 1 79693 YRDC yrdC N6-threonylcarbamoyltransferase domain containing

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 6.47e-01 4.39e-13 GO ribose phosphate diphosphokinase activity molecular_function 5.69e-01 2.62e-12 GO eukaryotic translation initiation factor 2B complex cellular_component 1.06e-01 6.55e-06 Reactome Heme biosynthesis Metabolism 9.95e-02 1.78e-04 GO EKC/KEOPS complex cellular_component 7.37e-02 2.62e-12 GO 5-phosphoribose 1-diphosphate biosynthetic process biological_process 4.05e-02 2.66e-05 GO positive regulation of mitochondrial translation biological_process 2.77e-02 1.04e-02 GO mRNA (2'-O-methyladenosine-N6-)-methyltransferase activity molecular_function 2.60e-02 5.30e-04 Reactome Synthesis of pyrophosphates in the cytosol Metabolism 2.59e-02 4.25e-04 Reactome tRNA modification in the mitochondrion Metabolism of RNA 2.17e-02 6.08e-08 GO tRNA binding molecular_function 1.73e-02 3.38e-07 Reactome tRNA modification in the nucleus and cytosol Metabolism of RNA 1.17e-02 6.47e-04 GO m7G(5')pppN diphosphatase activity molecular_function 1.06e-02 2.44e-11 Reactome Recycling of eIF2:GDP Metabolism of proteins 3.69e-03 1.39e-04 GO protein methylation 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 0.00e+00 0.00e+00 RNA modification 0.00e+00 0.00e+00 peptide biosynthetic process 0.00e+00 0.00e+00 tRNA metabolic process 0.00e+00 0.00e+00 translation 2.04e-11 1.81e-08 tRNA threonylcarbamoyladenosine metabolic process 2.76e-11 1.77e-08 ribose phosphate diphosphokinase activity 6.22e-11 3.86e-08 translation factor activity, RNA binding 6.45e-11 5.46e-08 tRNA modification 1.10e-10 9.08e-08 amide biosynthetic process 1.60e-10 8.04e-08 eukaryotic translation initiation factor 2B complex 6.29e-10 4.81e-07 regulation of translation 8.61e-10 6.46e-07 peptide metabolic process 1.25e-09 9.19e-07 negative regulation of translational initiation in response to stress 2.51e-09 1.78e-06 negative regulation of translation in response to stress 8.70e-09 5.70e-06 posttranscriptional regulation of gene expression 1.52e-08 9.67e-06 cellular amide metabolic process 1.54e-08 9.79e-06 tRNA processing 2.07e-08 1.29e-05 oligodendrocyte development 6.13e-08 3.58e-05 regulation of translation in response to stress 1.18e-07 3.97e-05 ribose phosphate diphosphokinase complex

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 1.78e-07 4.47e-05 TRANSLATION 2.13e-06 3.53e-04 TRANSLATION 2.26e-05 4.04e-03 METABOLISM OF PORPHYRINS 7.70e-04 7.95e-02 METABOLISM OF PORPHYRINS 1.62e-03 1.55e-01 MEMBRANE BINDING AND TARGETTING OF GAG PROTEINS 1.68e-03 1.60e-01 ACTIVATION OF CHAPERONES BY ATF6 ALPHA 1.78e-03 1.92e-01 METABOLISM OF CARBOHYDRATES 3.63e-03 3.50e-01 MEMBRANE BINDING AND TARGETTING OF GAG PROTEINS 3.67e-03 3.54e-01 LATE PHASE OF HIV LIFE CYCLE 3.68e-03 3.54e-01 HIV LIFE CYCLE 4.93e-03 4.06e-01 LATE PHASE OF HIV LIFE CYCLE 4.94e-03 4.06e-01 HIV LIFE CYCLE 5.67e-03 4.55e-01 METABOLISM OF CARBOHYDRATES 7.41e-03 6.30e-01 HIV INFECTION 1.09e-02 7.84e-01 HIV INFECTION 1.28e-02 9.68e-01 ACTIVATION OF CHAPERONES BY ATF6 ALPHA 2.58e-02 1.00e+00 UNFOLDED PROTEIN RESPONSE

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 2.11e-04 3.59e-01 decreased hemoglobin content 9.88e-04 8.96e-01 decreased mean corpuscular hemoglobin concentration 1.96e-03 1.00e+00 increased circulating free fatty acid level 2.29e-03 1.00e+00 decreased oxygen consumption 3.74e-03 1.00e+00 increased porphyrin level 3.75e-03 1.00e+00 jaundice 5.61e-03 1.00e+00 porphyria 5.61e-03 1.00e+00 leptocytosis 5.62e-03 1.00e+00 skeletal muscle degeneration 5.62e-03 1.00e+00 increased erythrocyte protoporphyrin level 7.48e-03 1.00e+00 absent retinal rod cells 7.48e-03 1.00e+00 hypochromic anemia 7.49e-03 1.00e+00 abnormal radial glial cell morphology 8.48e-03 1.00e+00 abnormal axon morphology 9.34e-03 1.00e+00 abnormal spinal cord dorsal column morphology 1.12e-02 1.00e+00 abnormal food preference 1.21e-02 1.00e+00 hypoactivity 1.31e-02 1.00e+00 abnormal axon fasciculation 1.31e-02 1.00e+00 increased oligodendrocyte number 1.31e-02 1.00e+00 skin photosensitivity

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

²FDR corrected p-value (Benjamini-Hochberg)