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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod361

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod361 Module size 66 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 60312 AFAP1 actin filament associated protein 1 186 AGTR2 angiotensin II receptor type 2 203859 ANO5 anoctamin 5 374 AREG amphiregulin 374 AREGB amphiregulin 84707 BEX1 brain expressed X-linked 2 55150 C19orf73 chromosome 19 open reading frame 73 857 CAV1 caveolin 1 51286 CEND1 cell cycle exit and neuronal differentiation 1 6320 CLEC11A C-type lectin domain containing 11A 123920 CMTM3 CKLF like MARVEL transmembrane domain containing 3 152189 CMTM8 CKLF like MARVEL transmembrane domain containing 8 22839 DLGAP4 DLG associated protein 4 64787 EPS8L2 EPS8 like 2 55179 FAIM Fas apoptotic inhibitory molecule 150946 FAM59B GRB2 associated regulator of MAPK1 subtype 2 55785 FGD6 FYVE, RhoGEF and PH domain containing 6 6573 FLOT1 solute carrier family 19 member 1 29909 GPR171 G protein-coupled receptor 171 60484 HAPLN2 hyaluronan and proteoglycan link protein 2 390992 HES3 hes family bHLH transcription factor 3 25998 IBTK inhibitor of Bruton tyrosine kinase 3490 IGFBP7 insulin like growth factor binding protein 7 3512 IGJ joining chain of multimeric IgA and IgM 146433 IL34 interleukin 34 3636 INPPL1 inositol polyphosphate phosphatase like 1 3630 INS insulin 3640 INSL3 insulin like 3 9856 KIAA0319 KIAA0319 23247 KIAA0556 KIAA0556 57648 KIAA1522 KIAA1522 3858 KRT10 keratin 10 3861 KRT14 keratin 14 3868 KRT16 keratin 16 3872 KRT17 keratin 17 3849 KRT2 keratin 2 319101 KRT73 keratin 73 3892 KRT86 keratin 86 3857 KRT9 keratin 9 84709 MGARP mitochondria localized glutamic acid rich protein 24225 NGF brain-derived neurotrophic factor 4909 NTF4 neurotrophin 4 4914 NTRK1 neurotrophic receptor tyrosine kinase 1 11333 PDAP1 PDGFA associated protein 1 5290 PIK3CA phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha 5291 PIK3CB phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit beta 5293 PIK3CD phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit delta 5294 PIK3CG phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit gamma 5783 PTPN13 protein tyrosine phosphatase, non-receptor type 13 10193 RNF41 ring finger protein 41 6276 S100A5 S100 calcium binding protein A5 8436 SDPR caveolae associated protein 2 84947 SERAC1 serine active site containing 1 6455 SH3GL1 SH3 domain containing GRB2 like 1, endophilin A2 6457 SH3GL3 SH3 domain containing GRB2 like 3, endophilin A3 51100 SH3GLB1 SH3 domain containing GRB2 like, endophilin B1 9187 SLC24A1 solute carrier family 24 member 1 257364 SNX33 sorting nexin 33 57537 SORCS2 sortilin related VPS10 domain containing receptor 2 200734 SPRED2 sprouty related EVH1 domain containing 2 283377 SPRYD4 SPRY domain containing 4 7024 TFCP2 transcription factor CP2 8711 TNK1 tyrosine kinase non receptor 1 7287 TULP1 tubby like protein 1 53347 UBASH3A ubiquitin associated and SH3 domain containing A 84959 UBASH3B ubiquitin associated and SH3 domain containing B

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 5.18e-01 1.12e-05 Reactome TRKA activation by NGF Signal Transduction 3.28e-01 4.07e-09 GO 1-phosphatidylinositol-4-phosphate 3-kinase activity molecular_function 1.17e-01 6.74e-03 Reactome NTF4 activates NTRK2 (TRKB) signaling Signal Transduction 7.46e-02 1.46e-08 Reactome PI3K/AKT activation Signal Transduction 3.09e-02 2.88e-05 GO intermediate filament organization biological_process 1.47e-02 3.71e-09 GO cornification biological_process 5.97e-03 2.61e-07 GO epidermis development biological_process 5.92e-03 8.53e-04 GO negative regulation of protein tyrosine kinase activity 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 3.17e-09 2.21e-06 cornification 8.74e-09 4.03e-06 1-phosphatidylinositol-4-phosphate 3-kinase activity 2.18e-08 1.36e-05 keratinization 4.14e-07 1.41e-04 phosphatidylinositol phosphate kinase activity 5.34e-07 2.67e-04 intermediate filament cytoskeleton organization 5.64e-07 2.81e-04 keratinocyte differentiation 6.38e-07 3.15e-04 intermediate filament-based process 8.75e-07 4.21e-04 intermediate filament organization 8.80e-07 2.60e-04 intermediate filament 1.57e-06 4.46e-04 phosphatidylinositol 3-kinase complex 2.63e-06 7.15e-04 intermediate filament cytoskeleton 4.92e-06 2.04e-03 epidermal cell differentiation 1.75e-05 4.35e-03 1-phosphatidylinositol-3-kinase activity 2.00e-05 7.17e-03 epidermis development 4.24e-05 1.39e-02 phosphatidylinositol biosynthetic process 4.74e-05 1.08e-02 structural molecule activity 6.37e-05 1.32e-02 early endosome membrane 6.69e-05 2.07e-02 skin development 7.05e-05 1.53e-02 neurotrophin p75 receptor binding 7.59e-05 1.63e-02 structural constituent of cytoskeleton

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 1.82e-08 3.88e-06 SYNTHESIS OF PIPS AT THE PLASMA MEMBRANE 1.09e-07 2.12e-05 PI METABOLISM 6.46e-07 1.50e-04 SYNTHESIS OF PIPS AT THE PLASMA MEMBRANE 2.12e-06 4.51e-04 PI METABOLISM 9.13e-06 1.37e-03 IL RECEPTOR SHC SIGNALING 2.12e-05 3.01e-03 PHOSPHOLIPID METABOLISM 8.99e-05 1.16e-02 IL 3 5 AND GM CSF SIGNALING 9.41e-05 1.21e-02 IL 2 SIGNALING 1.65e-04 1.99e-02 PI3K AKT ACTIVATION 1.68e-04 2.46e-02 IL RECEPTOR SHC SIGNALING 3.00e-04 3.43e-02 REGULATION OF SIGNALING BY CBL 4.98e-04 6.41e-02 PHOSPHOLIPID METABOLISM 9.77e-04 9.88e-02 GPVI MEDIATED ACTIVATION CASCADE 1.17e-03 1.35e-01 IL 2 SIGNALING 1.20e-03 1.38e-01 PI3K AKT ACTIVATION 1.22e-03 1.39e-01 IL 3 5 AND GM CSF SIGNALING 1.41e-03 1.58e-01 REGULATION OF SIGNALING BY CBL 2.64e-03 2.37e-01 SIGNALING BY ILS 3.79e-03 3.24e-01 CELL SURFACE INTERACTIONS AT THE VASCULAR WALL 3.87e-03 3.30e-01 NEPHRIN INTERACTIONS

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 5.58e-05 1.54e-01 abnormal pulmonary endothelial cell surface 8.11e-04 7.97e-01 increased vascular permeability 9.19e-04 8.57e-01 abnormal vascular endothelial cell morphology 1.02e-03 9.10e-01 abnormal myocardial fiber morphology 1.43e-03 1.00e+00 small superior cervical ganglion 1.84e-03 1.00e+00 abnormal sympathetic ganglion morphology 1.91e-03 1.00e+00 impaired neutrophil recruitment 1.97e-03 1.00e+00 thin interventricular septum 2.12e-03 1.00e+00 abnormal sensory neuron innervation pattern 2.22e-03 1.00e+00 abnormal milk composition 2.25e-03 1.00e+00 abnormal vasoconstriction 2.37e-03 1.00e+00 decreased sensory neuron number 2.41e-03 1.00e+00 abnormal heart left ventricle morphology 2.84e-03 1.00e+00 blepharoptosis 2.85e-03 1.00e+00 amyloid beta deposits 2.95e-03 1.00e+00 increased pancreatic beta cell number 3.40e-03 1.00e+00 insulin resistance 3.55e-03 1.00e+00 skin lesions 3.55e-03 1.00e+00 hypoalgesia 3.93e-03 1.00e+00 abnormal mammary gland alveolus morphology

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

²FDR corrected p-value (Benjamini-Hochberg)