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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod359

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod359 Module size 44 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 1244 ABCC2 ATP binding cassette subfamily C member 2 123624 AGBL1 ATP/GTP binding protein like 1 23287 AGTPBP1 ATP/GTP binding protein 1 10550 ARL6IP5 ADP ribosylation factor like GTPase 6 interacting protein 5 100910172 BASP1 brain acid soluble protein 1-like 790955 C11orf83 ubiquinol-cytochrome c reductase complex assembly factor 3 125988 C19orf70 chromosome 19 open reading frame 70 79095 C9orf16 chromosome 9 open reading frame 16 158055 C9orf163 chromosome 9 open reading frame 163 1604 CD55 CD55 molecule (Cromer blood group) 55573 CDV3 CDV3 homolog 1203 CLN5 CLN5, intracellular trafficking protein 58190 CTDSP1 CTD small phosphatase 1 10106 CTDSP2 CTD small phosphatase 2 10217 CTDSPL CTD small phosphatase like 23549 DAP aspartyl aminopeptidase 10613 ERLIN1 ER lipid raft associated 1 55177 FAM82A2 regulator of microtubule dynamics 3 2319 FLOT2 flotillin 2 2631 GBAS nipsnap homolog 2 51155 HN1 Jupiter microtubule associated homolog 1 121457 IKBIP IKBKB interacting protein 55004 LAMTOR1 late endosomal/lysosomal adaptor, MAPK and MTOR activator 1 28956 LAMTOR2 late endosomal/lysosomal adaptor, MAPK and MTOR activator 2 389541 LAMTOR4 late endosomal/lysosomal adaptor, MAPK and MTOR activator 4 137994 LETM2 leucine zipper and EF-hand containing transmembrane protein 2 64757 MARC1 mitochondrial amidoxime reducing component 1 57192 MCOLN1 mucolipin 1 8508 NIPSNAP1 nipsnap homolog 1 5445 PON2 paraoxonase 2 11230 PRAF2 PRA1 domain family member 2 51651 PTRH2 peptidyl-tRNA hydrolase 2 950 SCARB2 scavenger receptor class B member 2 29106 SCG3 secretogranin III 23677 SH3BP4 SH3 domain binding protein 4 91137 SLC25A46 solute carrier family 25 member 46 125170 SMCR7 mitochondrial elongation factor 2 55240 STEAP3 STEAP3 metalloreductase 55333 SYNJ2BP synaptojanin 2 binding protein 10548 TM9SF1 transmembrane 9 superfamily member 1 84233 TMEM126A transmembrane protein 126A 81542 TMX1 thioredoxin related transmembrane protein 1 84817 TXNDC17 thioredoxin domain containing 17 80139 ZNF703 zinc finger protein 703

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 2.11e-01 2.25e-07 GO CTD phosphatase activity molecular_function 2.51e-02 8.39e-06 Reactome mTORC1-mediated signalling Signal Transduction

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 1.69e-06 4.76e-04 Ragulator complex 1.19e-05 4.53e-03 autophagy 1.45e-05 5.39e-03 cellular response to amino acid stimulus 2.59e-05 9.02e-03 protein localization to lysosome 3.26e-05 1.10e-02 regulation of TOR signaling 3.46e-05 1.16e-02 C-terminal protein deglutamylation 3.68e-05 8.03e-03 late endosome membrane 3.87e-05 1.28e-02 positive regulation of TOR signaling 8.90e-05 1.88e-02 CTD phosphatase activity 1.03e-04 2.01e-02 late endosome 1.15e-04 3.29e-02 response to amino acid 1.77e-04 4.74e-02 protein side chain deglutamylation 1.94e-04 3.51e-02 lysosomal membrane 2.07e-04 3.88e-02 protein complex scaffold 2.26e-04 5.81e-02 protein deglutamylation 2.71e-04 6.77e-02 macroautophagy 3.60e-04 6.07e-02 vacuolar membrane 5.23e-04 8.39e-02 endosome membrane 6.50e-04 1.39e-01 negative regulation of G1/S transition of mitotic cell cycle 6.51e-04 1.39e-01 negative regulation of cell cycle G1/S phase transition

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 2.07e-05 2.95e-03 TRANSFERRIN ENDOCYTOSIS AND RECYCLING 3.54e-04 3.98e-02 IRON UPTAKE AND TRANSPORT 4.46e-04 5.82e-02 TRANSFERRIN ENDOCYTOSIS AND RECYCLING 1.11e-03 1.29e-01 IRON UPTAKE AND TRANSPORT 1.22e-02 8.65e-01 REGULATION OF COMPLEMENT CASCADE 1.46e-02 1.00e+00 TRANSMEMBRANE TRANSPORT OF SMALL MOLECULES 1.75e-02 1.00e+00 REGULATION OF COMPLEMENT CASCADE 2.00e-02 1.00e+00 ACTIVATION OF CHAPERONE GENES BY XBP1S 2.85e-02 1.00e+00 UNFOLDED PROTEIN RESPONSE 3.08e-02 1.00e+00 COMPLEMENT CASCADE 4.27e-02 1.00e+00 COMPLEMENT CASCADE

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 7.51e-04 7.64e-01 abnormal Schwann cell morphology 2.02e-03 1.00e+00 abnormal auditory brainstem response 3.20e-03 1.00e+00 abnormal retinal outer nuclear layer morphology 4.00e-03 1.00e+00 distended abdomen 5.41e-03 1.00e+00 thrombocytosis 6.28e-03 1.00e+00 abnormal nervous system morphology 6.65e-03 1.00e+00 increased rib number 7.47e-03 1.00e+00 decreased circulating copper level 7.47e-03 1.00e+00 leptocytosis 7.47e-03 1.00e+00 abnormal vestibular hair cell physiology 7.48e-03 1.00e+00 decreased splenocyte apoptosis 7.48e-03 1.00e+00 abnormal otolithic membrane morphology 9.33e-03 1.00e+00 increased liver copper level 9.34e-03 1.00e+00 abnormal reticulocyte morphology 9.34e-03 1.00e+00 abnormal cochlear VIII nucleus morphology 1.12e-02 1.00e+00 abnormal motor nerve collateral sprouting 1.12e-02 1.00e+00 abnormal mitral cell morphology 1.12e-02 1.00e+00 abnormal strial marginal cell morphology 1.12e-02 1.00e+00 abnormal ureter smooth muscle morphology 1.12e-02 1.00e+00 absent endocochlear potential

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

²FDR corrected p-value (Benjamini-Hochberg)