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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod252

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod252 Module size 57 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 57001 ACN9 succinate dehydrogenase complex assembly factor 3 51027 BOLA1 bolA family member 1 54987 C1orf123 chromosome 1 open reading frame 123 708 C1QBP complement C1q binding protein 55969 C20orf24 RAB5 interacting factor 51250 C6orf203 chromosome 6 open reading frame 203 90871 C9orf123 distal membrane arm assembly complex 1 131076 CCDC58 coiled-coil domain containing 58 91612 CHURC1 churchill domain containing 1 284106 CISD3 CDGSH iron sulfur domain 3 2776 CMC1 G protein subunit alpha q 56942 CMC2 C-X9-C motif containing 2 493753 COA5 cytochrome c oxidase assembly factor 5 295238 DAP3 death associated protein 3 300514 EI24 EI24, autophagy associated transmembrane protein 79675 FASTKD1 FAST kinase domains 1 22868 FASTKD2 FAST kinase domains 2 26515 FXC1 translocase of inner mitochondrial membrane 10B 2926 GRSF1 G-rich RNA sequence binding factor 1 25764 HYPK huntingtin interacting protein K 3609 ILF3 interleukin enhancer binding factor 3 57707 KIAA1609 MTOR associated protein, eak-7 homolog 65108 MARCKSL1 MARCKS like 1 28985 MCTS1 MCTS1, re-initiation and release factor 29074 MRPL18 mitochondrial ribosomal protein L18 54148 MRPL39 mitochondrial ribosomal protein L39 84311 MRPL45 mitochondrial ribosomal protein L45 116540 MRPL53 mitochondrial ribosomal protein L53 56945 MRPS22 mitochondrial ribosomal protein S22 23107 MRPS27 mitochondrial ribosomal protein S27 10884 MRPS30 mitochondrial ribosomal protein S30 10240 MRPS31 mitochondrial ribosomal protein S31 65993 MRPS34 mitochondrial ribosomal protein S34 92259 MRPS36 mitochondrial ribosomal protein S36 51335 NGRN neugrin, neurite outgrowth associated 9141 PDCD5 programmed cell death 5 5037 PEBP1 phosphatidylethanolamine binding protein 1 5204 PFDN5 prefoldin subunit 5 9374 PPT2 palmitoyl-protein thioesterase 2 112464 PRKCDBP caveolae associated protein 3 55037 PTCD3 pentatricopeptide repeat domain 3 391356 PTRHD1 peptidyl-tRNA hydrolase domain containing 1 1468 SLC25A10 solute carrier family 25 member 10 440957 SMIM4 small integral membrane protein 4 6742 SSBP1 single stranded DNA binding protein 1 79736 TEFM transcription elongation factor, mitochondrial 26519 TIMM10 translocase of inner mitochondrial membrane 10 26517 TIMM13 translocase of inner mitochondrial membrane 13 1678 TIMM8A translocase of inner mitochondrial membrane 8A 26521 TIMM8B translocase of inner mitochondrial membrane 8 homolog B 26520 TIMM9 translocase of inner mitochondrial membrane 9 10430 TMEM147 transmembrane protein 147 79064 TMEM223 transmembrane protein 223 54968 TMEM70 transmembrane protein 70 100528016 TMX2-CTNND1 TMX2-CTNND1 readthrough (NMD candidate) 9540 TP53I3 tumor protein p53 inducible protein 3 51398 WDR83OS WD repeat domain 83 opposite strand

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 1.66e-01 5.11e-07 GO protein import into mitochondrial inner membrane biological_process 9.29e-02 4.25e-08 GO positive regulation of mitochondrial translation biological_process 3.97e-02 2.99e-11 GO mitochondrial small ribosomal subunit cellular_component 3.10e-02 2.01e-04 GO mitochondrial DNA replication biological_process 2.02e-02 2.89e-19 GO mitochondrial translational termination biological_process 1.89e-02 2.89e-19 GO mitochondrial translational elongation biological_process 1.38e-02 4.92e-09 Reactome Mitochondrial protein import Metabolism of proteins 1.30e-02 3.83e-19 Reactome Mitochondrial translation initiation Metabolism of proteins 7.35e-03 3.83e-19 Reactome Mitochondrial translation elongation Metabolism of proteins 6.42e-03 2.94e-04 GO ribonucleoprotein granule cellular_component 5.16e-03 3.83e-19 Reactome Mitochondrial translation termination Metabolism of proteins 3.79e-03 5.50e-07 GO protein targeting to mitochondrion 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 mitochondrial membrane 0.00e+00 0.00e+00 mitochondrial envelope 0.00e+00 0.00e+00 mitochondrial inner membrane 0.00e+00 0.00e+00 organelle inner membrane 3.29e-11 2.86e-08 chaperone-mediated protein transport 8.28e-11 6.93e-08 mitochondrial translational termination 8.28e-11 6.93e-08 mitochondrial translational elongation 1.69e-10 1.37e-07 translational termination 2.36e-10 1.89e-07 translational elongation 3.46e-10 2.72e-07 mitochondrial translation 4.76e-10 3.68e-07 protein complex disassembly 9.75e-10 4.38e-07 mitochondrial matrix 3.26e-09 2.27e-06 translation 5.20e-09 2.13e-06 mitochondrial intermembrane space protein transporter complex 5.68e-09 3.81e-06 peptide biosynthetic process 1.32e-08 8.46e-06 amide biosynthetic process 2.86e-08 1.07e-05 ribosome 3.76e-08 2.26e-05 peptide metabolic process 4.42e-08 1.62e-05 intracellular ribonucleoprotein complex 4.44e-08 1.62e-05 ribonucleoprotein complex

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 1.12e-08 3.26e-06 MITOCHONDRIAL PROTEIN IMPORT 3.58e-07 6.60e-05 MITOCHONDRIAL PROTEIN IMPORT 3.63e-03 3.13e-01 GLUCONEOGENESIS 9.84e-03 7.91e-01 INTRINSIC PATHWAY 1.20e-02 8.53e-01 GLUCOSE METABOLISM 1.31e-02 9.85e-01 AMINO ACID AND OLIGOPEPTIDE SLC TRANSPORTERS 1.65e-02 1.00e+00 INTRINSIC PATHWAY 1.83e-02 1.00e+00 FORMATION OF FIBRIN CLOT CLOTTING CASCADE 2.11e-02 1.00e+00 GLUCONEOGENESIS 2.34e-02 1.00e+00 AMINO ACID AND OLIGOPEPTIDE SLC TRANSPORTERS 2.48e-02 1.00e+00 SULFUR AMINO ACID METABOLISM 2.64e-02 1.00e+00 PREFOLDIN MEDIATED TRANSFER OF SUBSTRATE TO CCT TRIC 2.83e-02 1.00e+00 SULFUR AMINO ACID METABOLISM 2.98e-02 1.00e+00 PREFOLDIN MEDIATED TRANSFER OF SUBSTRATE TO CCT TRIC 3.89e-02 1.00e+00 GLUCOSE METABOLISM 4.84e-02 1.00e+00 FORMATION OF FIBRIN CLOT CLOTTING CASCADE

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 1.54e-03 1e+00 decreased brain weight 3.74e-03 1e+00 abnormal retina outer limiting membrane morphology 3.74e-03 1e+00 necrospermia 3.74e-03 1e+00 abnormal pancreatic acinar cell zymogen granule morphology 5.61e-03 1e+00 abnormal cerebellum white matter morphology 5.61e-03 1e+00 abnormal placenta size 7.18e-03 1e+00 abnormal retina morphology 7.47e-03 1e+00 enlarged pancreas 7.47e-03 1e+00 abnormal gastric gland morphology 7.47e-03 1e+00 lipodystrophy 7.48e-03 1e+00 abnormal intercostal muscle morphology 8.28e-03 1e+00 hydroencephaly 8.35e-03 1e+00 abnormal brain morphology 8.81e-03 1e+00 decreased fibroblast apoptosis 9.34e-03 1e+00 decreased total retina thickness 1.12e-02 1e+00 lipofuscinosis 1.12e-02 1e+00 abnormal urinary bladder urothelium morphology 1.12e-02 1e+00 jerky movement 1.12e-02 1e+00 abnormal exocrine pancreas morphology 1.12e-02 1e+00 tachypnea

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

²FDR corrected p-value (Benjamini-Hochberg)