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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod360

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod360 Module size 61 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 10939 AFG3L2 AFG3 like matrix AAA peptidase subunit 2 55515 ASIC4 acid sensing ion channel subunit family member 4 51802 ASIC5 acid sensing ion channel subunit family member 5 617 BCS1L BCS1 homolog, ubiquinol-cytochrome c reductase complex chaperone 254863 C17orf61 transmembrane protein 256 91689 C22orf32 single-pass membrane protein with aspartate rich tail 1 401466 C8orf59 chromosome 8 open reading frame 59 293485 CLN3 CLN3, battenin 51287 COA4 cytochrome c oxidase assembly factor 4 homolog 90639 COX19 cytochrome c oxidase assembly factor COX19 54675 CRLS1 cardiolipin synthase 1 51496 CTDSPL2 CTD small phosphatase like 2 129080 EMID1 EMI domain containing 1 26355 FAM162A family with sequence similarity 162 member A 10447 FAM3C family with sequence similarity 3 member C 2395 FXN frataxin 2671 GFER growth factor, augmenter of liver regeneration 27069 GHITM growth hormone inducible transmembrane protein 8225 GTPBP6 GTP binding protein 6 (putative) 305457 LETM1 leucine zipper and EF-hand containing transmembrane protein 1 388789 LINC00493 small integral membrane protein 26 57128 LYRM4 LYR motif containing 4 115416 MALSU1 mitochondrial assembly of ribosomal large subunit 1 84769 MPV17L2 MPV17 mitochondrial inner membrane protein like 2 23787 MTCH1 mitochondrial carrier 1 23788 MTCH2 mitochondrial carrier 2 51001 MTERFD1 mitochondrial transcription termination factor 3 7827 NPHS2 NPHS2, podocin 27020 NPTN neuroplastin 283927 NUDT7 nudix hydrolase 7 254552 NUDT8 nudix hydrolase 8 5245 PHB prohibitin 11331 PHB2 prohibitin 2 10105 PPIF peptidylprolyl isomerase F 140823 ROMO1 reactive oxygen species modulator 1 9997 SCO2 SCO2, cytochrome c oxidase assembly protein 54949 SDHAF2 succinate dehydrogenase complex assembly factor 2 118980 SFXN2 sideroflexin 2 119559 SFXN4 sideroflexin 4 8402 SLC25A11 solute carrier family 25 member 11 8604 SLC25A12 solute carrier family 25 member 12 83733 SLC25A18 solute carrier family 25 member 18 79751 SLC25A22 solute carrier family 25 member 22 79085 SLC25A23 solute carrier family 25 member 23 29957 SLC25A24 solute carrier family 25 member 24 114789 SLC25A25 solute carrier family 25 member 25 54977 SLC25A38 solute carrier family 25 member 38 291 SLC25A4 solute carrier family 25 member 4 284427 SLC25A41 solute carrier family 25 member 41 292 SLC25A5 solute carrier family 25 member 5 54471 SMCR7L mitochondrial elongation factor 1 79622 SNRNP25 small nuclear ribonucleoprotein U11/U12 subunit 25 6687 SPG7 SPG7, paraplegin matrix AAA peptidase subunit 2040 STOM stomatin 9399 STOML1 stomatin like 1 30968 STOML2 stomatin like 2 161003 STOML3 stomatin like 3 81853 TMEM14B transmembrane protein 14B 29100 TMEM208 transmembrane protein 208 51499 TRIAP1 TP53 regulated inhibitor of apoptosis 1 10730 YME1L1 YME1 like 1 ATPase

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 4.44e-01 3.09e-03 Reactome Synthesis of CL Metabolism 3.51e-01 2.94e-13 GO ATP transport biological_process 1.26e-01 5.04e-12 Reactome Processing of SMDT1 Transport of small molecules 1.24e-01 2.30e-06 GO aspartate transmembrane transport biological_process 8.46e-02 1.98e-13 GO mitochondrial calcium ion transmembrane transport biological_process 5.06e-02 5.98e-06 GO L-glutamate transmembrane transporter activity molecular_function 4.29e-02 1.83e-05 GO negative regulation of release of cytochrome c from mitochondria biological_process 4.27e-02 4.16e-13 Reactome Mitochondrial calcium ion transport Transport of small molecules 3.63e-02 2.19e-05 GO mitochondrial respiratory chain complex IV assembly biological_process 1.08e-02 1.07e-09 Reactome Mitochondrial protein import Metabolism of proteins 8.49e-03 6.05e-04 Reactome Mitochondrial iron-sulfur cluster biogenesis Metabolism 3.86e-03 1.27e-08 GO mitochondrion organization 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 mitochondrion organization 0.00e+00 0.00e+00 mitochondrial transport 0.00e+00 0.00e+00 ATP transport 0.00e+00 0.00e+00 ADP transport 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 0.00e+00 0.00e+00 organic anion transmembrane transporter activity 0.00e+00 0.00e+00 ADP transmembrane transporter activity 0.00e+00 0.00e+00 ATP transmembrane transporter activity 2.73e-12 1.86e-09 adenine nucleotide transmembrane transporter activity 3.67e-12 3.36e-09 adenine nucleotide transport 3.75e-12 2.54e-09 purine nucleotide transmembrane transporter activity 6.00e-12 5.44e-09 purine ribonucleotide transport 8.68e-12 7.83e-09 purine nucleotide transport 3.77e-10 2.15e-07 nucleobase-containing compound transmembrane transporter activity 6.06e-10 4.64e-07 organic anion transport 2.26e-09 1.13e-06 anion transmembrane transporter activity 8.18e-09 5.37e-06 carbohydrate derivative transport

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 6.27e-08 1.66e-05 MITOCHONDRIAL PROTEIN IMPORT 5.42e-07 9.87e-05 MITOCHONDRIAL PROTEIN IMPORT 4.76e-05 7.97e-03 INTERACTIONS OF VPR WITH HOST CELLULAR PROTEINS 5.02e-05 6.72e-03 INTERACTIONS OF VPR WITH HOST CELLULAR PROTEINS 3.24e-04 4.39e-02 HOST INTERACTIONS OF HIV FACTORS 4.15e-04 5.47e-02 GLUCONEOGENESIS 4.39e-04 4.82e-02 HOST INTERACTIONS OF HIV FACTORS 9.88e-04 1.17e-01 REGULATION OF INSULIN SECRETION 1.22e-03 1.20e-01 GLUCONEOGENESIS 1.37e-03 1.54e-01 GLUCOSE METABOLISM 1.85e-03 1.99e-01 INTEGRATION OF ENERGY METABOLISM 1.86e-03 1.75e-01 REGULATION OF INSULIN SECRETION 2.36e-03 2.15e-01 HIV INFECTION 3.32e-03 3.27e-01 HIV INFECTION 3.59e-03 3.10e-01 GLUCOSE METABOLISM 3.85e-03 3.29e-01 INTEGRATION OF ENERGY METABOLISM 6.96e-03 5.45e-01 ACYL CHAIN REMODELLING OF PG 1.17e-02 9.02e-01 ACYL CHAIN REMODELLING OF PG 1.32e-02 9.91e-01 METABOLISM OF CARBOHYDRATES 4.22e-02 1.00e+00 METABOLISM OF CARBOHYDRATES

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 1.29e-04 2.68e-01 abnormal mitochondrial physiology 2.76e-04 4.29e-01 increased circulating lactate level 3.01e-04 4.47e-01 abnormal aerobic respiration 4.92e-04 6.01e-01 increased mitochondria size 8.05e-04 7.93e-01 abnormal mitochondrial ATP synthesis coupled electron transport 1.71e-03 1.00e+00 abnormal locomotor activation 3.74e-03 1.00e+00 abnormal exercise endurance 4.53e-03 1.00e+00 complete embryonic lethality between implantation and placentation 5.00e-03 1.00e+00 impaired coordination 5.19e-03 1.00e+00 gliosis 5.32e-03 1.00e+00 muscle weakness 5.61e-03 1.00e+00 podocyte hypertrophy 5.61e-03 1.00e+00 abnormal kidney arterial blood vessel morphology 5.61e-03 1.00e+00 abnormal peritubular capillary morphology 5.65e-03 1.00e+00 decreased urine urea nitrogen level 5.76e-03 1.00e+00 tremors 7.10e-03 1.00e+00 hunched posture 7.37e-03 1.00e+00 abnormal proximal convoluted tubule morphology 7.80e-03 1.00e+00 axon degeneration 8.25e-03 1.00e+00 abnormal myelination

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

²FDR corrected p-value (Benjamini-Hochberg)