Back to main page

DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod326

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod326 Module size 48 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 144568 A2ML1 alpha-2-macroglobulin like 1 114506 ANKH ANKH inorganic pyrophosphate transport regulator 345 APOC3 apolipoprotein C3 348 APOE apolipoprotein E 135152 B3GAT2 beta-1,3-glucuronyltransferase 2 54862 CC2D1A coiled-coil and C2 domain containing 1A 154790 CLEC2L C-type lectin domain family 2 member L 80315 CPEB4 cytoplasmic polyadenylation element binding protein 4 8029 CUBN cubilin 1634 DCN decorin 9228 DLGAP2 DLG associated protein 2 116662 ECM1 extracellular matrix protein 1 2134 EXTL1 exostosin like glycosyltransferase 1 2137 EXTL3 exostosin like glycosyltransferase 3 339479 FAM5C BMP/retinoic acid inducible neural specific 3 10755 GIPC1 GIPC PDZ domain containing family member 1 2817 GPC1 glypican 1 57549 IGSF9 immunoglobulin superfamily member 9 9118 INA internexin neuronal intermediate filament protein alpha 9270 ITGB1BP1 integrin subunit beta 1 binding protein 1 3730 KAL1 anosmin 1 90070 LACRT lacritin 3949 LDLR low density lipoprotein receptor 26119 LDLRAP1 low density lipoprotein receptor adaptor protein 1 4035 LRP1 LDL receptor related protein 1 4036 LRP2 LDL receptor related protein 2 4038 LRP4 LDL receptor related protein 4 7804 LRP8 LDL receptor related protein 8 4043 LRPAP1 LDL receptor related protein associated protein 1 9479 MAPK8IP1 mitogen-activated protein kinase 8 interacting protein 1 266727 MDGA1 MAM domain containing glycosylphosphatidylinositol anchor 1 4481 MSR1 macrophage scavenger receptor 1 4744 NEFH neurofilament heavy 4741 NEFM neurofilament medium 4818 NKG7 natural killer cell granule protein 7 84309 NUDT16L1 nudix hydrolase 16 like 1 200150 PLD5 phospholipase D family member 5 5446 PON3 paraoxonase 3 5764 PTN pleiotrophin 5947 RBP1 retinol binding protein 1 795 S100G S100 calcium binding protein G 57823 SLAMF7 SLAM family member 7 9784 SNX17 sorting nexin 17 6948 TCN2 transcobalamin 2 7093 TLL2 tolloid like 2 9911 TMCC2 transmembrane and coiled-coil domain family 2 10103 TSPAN1 tetraspanin 1 7436 VLDLR very low density lipoprotein receptor

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 4.42e-01 2.62e-03 Reactome Defective TCN2 causes hereditary megaloblastic anemia Disease 1.50e-01 1.24e-10 GO low-density lipoprotein particle receptor activity molecular_function 1.25e-01 2.01e-05 Reactome Chylomicron clearance Transport of small molecules 8.07e-02 2.73e-06 GO amyloid precursor protein metabolic process biological_process 6.50e-02 4.04e-08 GO lipoprotein transport biological_process 6.31e-02 5.49e-08 GO apolipoprotein binding molecular_function 4.69e-02 1.90e-13 Reactome Retinoid metabolism and transport Metabolism#Signal Transduction 4.02e-02 2.73e-06 GO amyloid-beta clearance biological_process 4.01e-02 9.32e-07 GO chylomicron remnant clearance biological_process 3.53e-02 2.38e-07 GO low-density lipoprotein particle receptor binding molecular_function 9.89e-03 4.20e-07 GO positive regulation of endocytosis biological_process 6.99e-03 7.84e-03 Reactome Defective AMN causes hereditary megaloblastic anemia 1 Disease 1.48e-03 7.84e-03 Reactome Defective CUBN causes hereditary megaloblastic anemia 1 Disease

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 4.36e-10 3.39e-07 plasma lipoprotein particle clearance 8.36e-10 3.80e-07 neurofilament 2.10e-09 1.50e-06 receptor-mediated endocytosis 2.87e-09 1.42e-06 lipoprotein particle receptor binding 5.58e-09 2.63e-06 low-density lipoprotein receptor activity 1.82e-08 1.14e-05 retinoid metabolic process 3.89e-08 2.34e-05 diterpenoid metabolic process 3.89e-08 2.34e-05 regulation of plasma lipoprotein particle levels 7.87e-08 3.07e-05 cargo receptor activity 1.66e-07 6.14e-05 lipoprotein particle binding 2.50e-07 1.32e-04 isoprenoid metabolic process 3.75e-07 1.93e-04 lipoprotein transport 5.07e-07 2.55e-04 endocytosis 5.91e-07 2.93e-04 positive regulation of postsynaptic membrane organization 7.43e-07 3.62e-04 lipoprotein metabolic process 8.09e-07 2.40e-04 plasma lipoprotein particle 9.95e-07 2.91e-04 protein-lipid complex 1.53e-06 7.03e-04 cholesterol transport 1.66e-06 5.06e-04 very-low-density lipoprotein particle receptor activity 1.81e-06 8.20e-04 cholesterol metabolic process

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 7.61e-09 1.69e-06 LIPOPROTEIN METABOLISM 3.63e-08 9.90e-06 LIPOPROTEIN METABOLISM 6.12e-08 1.22e-05 LIPID DIGESTION MOBILIZATION AND TRANSPORT 6.19e-08 1.24e-05 CHYLOMICRON MEDIATED LIPID TRANSPORT 2.13e-07 5.31e-05 CHYLOMICRON MEDIATED LIPID TRANSPORT 2.17e-07 5.40e-05 LIPID DIGESTION MOBILIZATION AND TRANSPORT 8.53e-06 1.29e-03 HDL MEDIATED LIPID TRANSPORT 1.26e-05 2.37e-03 A TETRASACCHARIDE LINKER SEQUENCE IS REQUIRED FOR GAG SYNTHESIS 2.27e-05 4.05e-03 HDL MEDIATED LIPID TRANSPORT 5.38e-05 7.20e-03 A TETRASACCHARIDE LINKER SEQUENCE IS REQUIRED FOR GAG SYNTHESIS 3.00e-04 3.43e-02 CHONDROITIN SULFATE DERMATAN SULFATE METABOLISM 3.76e-04 5.01e-02 CHONDROITIN SULFATE DERMATAN SULFATE METABOLISM 4.87e-04 5.30e-02 HEPARAN SULFATE HEPARIN HS GAG METABOLISM 5.96e-04 7.51e-02 HEPARAN SULFATE HEPARIN HS GAG METABOLISM 3.01e-03 2.66e-01 STEROID HORMONES 3.44e-03 2.99e-01 METABOLISM OF STEROID HORMONES AND VITAMINS A AND D 3.98e-03 3.38e-01 GLYCOSAMINOGLYCAN METABOLISM 4.42e-03 4.13e-01 STEROID HORMONES 5.44e-03 4.90e-01 GLYCOSAMINOGLYCAN METABOLISM 6.53e-03 5.69e-01 METABOLISM OF STEROID HORMONES AND VITAMINS A AND D

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 5.72e-06 3.17e-02 abnormal circulating LDL cholesterol level 1.82e-04 3.30e-01 persistent truncus arteriosus type i 3.92e-04 5.25e-01 abnormal synapse morphology 5.68e-04 6.56e-01 abnormal retinal pigment epithelium morphology 8.03e-04 7.93e-01 increased cardiac output 1.00e-03 9.02e-01 increased susceptibility to atherosclerosis 1.20e-03 1.00e+00 atherosclerotic lesions 1.52e-03 1.00e+00 increased circulating LDL cholesterol level 1.57e-03 1.00e+00 retinal neovascularization 1.62e-03 1.00e+00 abnormal Bruch membrane morphology 1.91e-03 1.00e+00 abnormal circulating protein level 1.92e-03 1.00e+00 increased circulating VLDL triglyceride level 2.82e-03 1.00e+00 increased circulating triglyceride level 3.18e-03 1.00e+00 amyloid beta deposits 3.38e-03 1.00e+00 increased circulating cholesterol level 3.52e-03 1.00e+00 abnormal tendon morphology 4.72e-03 1.00e+00 abnormal triglyceride level 5.47e-03 1.00e+00 abnormal circulating enzyme level 5.51e-03 1.00e+00 oxidative stress 5.60e-03 1.00e+00 increased circulating VLDL cholesterol level

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

²FDR corrected p-value (Benjamini-Hochberg)