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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod156

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod156 Module size 58 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 145447 ABHD12B abhydrolase domain containing 12B 9465 AKAP7 A-kinase anchoring protein 7 57679 ALS2 ALS2, alsin Rho guanine nucleotide exchange factor 143872 ARHGAP42 Rho GTPase activating protein 42 51008 ASCC1 activating signal cointegrator 1 complex subunit 1 283897 C16orf54 chromosome 16 open reading frame 54 54953 C1orf27 odr-4 GPCR localization factor homolog 388389 CCDC103 coiled-coil domain containing 103 196477 CCER1 coiled-coil glutamate rich protein 1 9731 CEP104 centrosomal protein 104 497190 CLEC18B C-type lectin domain family 18 member B 283971 CLEC18C C-type lectin domain family 18 member C 51232 CRIM1 cysteine rich transmembrane BMP regulator 1 25861 DFNB31 whirlin 26052 DNM3 dynamin 3 84067 FAM160A2 family with sequence similarity 160 member A2 54754 FAM22F NUT family member 2F 85462 FHDC1 FH2 domain containing 1 51454 GULP1 GULP PTB domain containing engulfment adaptor 1 51361 HOOK1 hook microtubule tethering protein 1 29911 HOOK2 hook microtubule tethering protein 2 84376 HOOK3 hook microtubule tethering protein 3 64423 INF2 inverted formin, FH2 and WH2 domain containing 3860 KRT13 keratin 13 121391 KRT74 keratin 74 3856 KRT8 keratin 8 3931 LCAT lecithin-cholesterol acyltransferase 91289 LMF2 lipase maturation factor 2 729967 MORN2 MORN repeat containing 2 254956 MORN5 MORN repeat containing 5 22989 MYH15 myosin heavy chain 15 57644 MYH7B myosin heavy chain 7B 4651 MYO10 myosin X 399687 MYO18A myosin XVIIIA 84700 MYO18B myosin XVIIIB 4643 MYO1C myosin IE 4644 MYO5A myosin VA 4649 MYO9A myosin IXA 4650 MYO9B myosin IXB 123803 NTAN1 N-terminal asparagine amidase 57624 NYAP2 neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adaptor 2 255738 PCSK9 proprotein convertase subtilisin/kexin type 9 5255 PHKA1 phosphorylase kinase regulatory subunit alpha 1 221476 PI16 peptidase inhibitor 16 196463 PLBD2 phospholipase B domain containing 2 5359 PLSCR1 phospholipid scramblase 1 57088 PLSCR4 phospholipid scramblase 4 203069 R3HCC1 R3H domain and coiled-coil containing 1 27291 R3HCC1L R3H domain and coiled-coil containing 1 like 353116 RILPL1 Rab interacting lysosomal protein like 1 196383 RILPL2 Rab interacting lysosomal protein like 2 51150 SDF4 stromal cell derived factor 4 64093 SMOC1 SPARC related modular calcium binding 1 83985 SPNS1 sphingolipid transporter 1 (putative) 84260 TCHP trichoplein keratin filament binding 26022 TMEM98 transmembrane protein 98 402682 UFSP1 UFM1 specific peptidase 1 (inactive) 55325 UFSP2 UFM1 specific peptidase 2

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 8.78e-02 7.80e-08 GO cytoskeleton-dependent intracellular transport biological_process 5.88e-02 2.21e-04 GO phospholipid scrambling biological_process 4.20e-02 1.73e-08 GO dynein light intermediate chain binding molecular_function 3.71e-02 1.73e-05 GO microfilament motor activity molecular_function 3.50e-02 4.12e-07 GO early endosome to late endosome transport biological_process 2.22e-02 7.16e-08 GO endosome organization biological_process 2.20e-02 7.77e-06 GO HOPS complex cellular_component 1.32e-02 3.60e-07 GO motor 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 0.00e+00 0.00e+00 myosin complex 4.17e-10 2.36e-07 dynein light intermediate chain binding 2.21e-09 9.54e-07 FHF complex 1.09e-08 4.94e-06 motor activity 1.98e-08 8.63e-06 actin binding 3.80e-08 2.29e-05 endomembrane system organization 3.14e-07 1.63e-04 early endosome to late endosome transport 9.25e-07 2.95e-04 microfilament motor activity 1.17e-06 5.49e-04 endosome organization 2.69e-06 7.85e-04 small GTPase binding 2.97e-06 1.29e-03 lysosomal transport 5.56e-06 1.53e-03 GTPase binding 7.31e-06 2.92e-03 endosome to lysosome transport 8.49e-06 2.11e-03 supramolecular fiber 1.11e-05 4.26e-03 vacuolar transport 1.24e-05 4.70e-03 lysosome organization 1.28e-05 3.27e-03 calmodulin binding 1.59e-05 3.99e-03 nucleoside-triphosphatase activity 1.76e-05 6.42e-03 vesicle organization 1.82e-05 4.22e-03 unconventional myosin complex

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 9.66e-03 7.14e-01 SIGNALING BY FGFR1 FUSION MUTANTS 9.68e-03 7.14e-01 SIGNALING BY FGFR1 MUTANTS 9.71e-03 7.15e-01 SIGNALING BY FGFR MUTANTS 1.31e-02 9.12e-01 HDL MEDIATED LIPID TRANSPORT 1.50e-02 1.00e+00 SIGNALING BY FGFR IN DISEASE 1.53e-02 1.00e+00 SIGNALING BY FGFR1 MUTANTS 1.53e-02 1.00e+00 SIGNALING BY FGFR1 FUSION MUTANTS 1.54e-02 1.00e+00 SIGNALING BY FGFR MUTANTS 1.55e-02 1.00e+00 SIGNALING BY FGFR IN DISEASE 1.70e-02 1.00e+00 HDL MEDIATED LIPID TRANSPORT 1.88e-02 1.00e+00 GLYCOGEN BREAKDOWN GLYCOGENOLYSIS 2.15e-02 1.00e+00 GLYCOGEN BREAKDOWN GLYCOGENOLYSIS 2.20e-02 1.00e+00 INSULIN SYNTHESIS AND PROCESSING 2.32e-02 1.00e+00 LIPOPROTEIN METABOLISM 2.74e-02 1.00e+00 LIPOPROTEIN METABOLISM 2.86e-02 1.00e+00 INSULIN SYNTHESIS AND PROCESSING 3.15e-02 1.00e+00 NETRIN1 SIGNALING 3.46e-02 1.00e+00 NETRIN1 SIGNALING 3.70e-02 1.00e+00 LIPID DIGESTION MOBILIZATION AND TRANSPORT 4.58e-02 1.00e+00 GLUCOSE METABOLISM

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 6.15e-05 1.63e-01 abnormal tail pigmentation 1.43e-04 2.88e-01 iris coloboma 6.66e-04 7.18e-01 syndactyly 1.70e-03 1.00e+00 abnormal coat/hair pigmentation 3.69e-03 1.00e+00 abnormal locomotor coordination 6.19e-03 1.00e+00 abnormal cholesterol homeostasis 7.48e-03 1.00e+00 abnormal interdigital cell death 7.50e-03 1.00e+00 abnormal epidermal melanocyte morphology 9.33e-03 1.00e+00 abnormal dorsoventral coat patterning 9.34e-03 1.00e+00 abnormal hair follicle melanin granule morphology 9.36e-03 1.00e+00 decreased circulating creatine kinase level 9.36e-03 1.00e+00 retina coloboma 9.36e-03 1.00e+00 abnormal vestibular hair cell physiology 9.38e-03 1.00e+00 abnormal eye posterior chamber morphology 9.38e-03 1.00e+00 impaired ureteric peristalsis 1.21e-02 1.00e+00 internal hemorrhage 1.26e-02 1.00e+00 increased circulating HDL cholesterol level 1.30e-02 1.00e+00 abnormal manchette morphology 1.31e-02 1.00e+00 glomerulosclerosis 1.31e-02 1.00e+00 fetal bleb

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

²FDR corrected p-value (Benjamini-Hochberg)