Back to main page

DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod24

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod24 Module size 31 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 325 APCS amyloid P component, serum 335 APOA1 apolipoprotein A1 80350 APOA2 lipoprotein(a) like 2, pseudogene 337 APOA4 apolipoprotein A4 116519 APOA5 apolipoprotein A5 338 APOB apolipoprotein B 341 APOC1 apolipoprotein C1 344 APOC2 apolipoprotein C2 347 APOD apolipoprotein D 319 APOF apolipoprotein F 1071 CETP cholesteryl ester transfer protein 339390 CLEC4G C-type lectin domain family 4 member G 1471 CST3 cystatin C 2934 GSN gelsolin 55600 ITLN1 intelectin 1 9445 ITM2B integral membrane protein 2B 3933 LCN1 lipocalin 1 4057 LTF lactotransferrin 4069 LYZ lysozyme 4240 MFGE8 milk fat globule-EGF factor 8 protein 4504 MT3 metallothionein 3 4547 MTTP microsomal triglyceride transfer protein 4878 NPPA natriuretic peptide A 54959 ODAM odontogenic, ameloblast associated 5360 PLTP phospholipid transfer protein 5950 RBP4 retinol binding protein 4 949 SCARB1 scavenger receptor class B member 1 6406 SEMG1 semenogelin 1 64220 STRA6 stimulated by retinoic acid 6 7045 TGFBI transforming growth factor beta induced 7276 TTR transthyretin

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 3.42e-01 1.80e-03 Reactome Retinoid metabolism disease events Disease 1.34e-01 9.45e-06 Reactome LDL remodeling Transport of small molecules 1.04e-01 2.19e-26 Reactome Amyloid fiber formation Metabolism of proteins 1.02e-01 5.31e-08 Reactome VLDL assembly Transport of small molecules 9.67e-02 1.01e-18 GO high-density lipoprotein particle remodeling biological_process 7.97e-02 1.30e-10 GO lipase inhibitor activity molecular_function 7.60e-02 3.44e-15 GO lipid transporter activity molecular_function 6.71e-02 1.02e-16 GO chylomicron cellular_component 6.54e-02 1.73e-15 GO chylomicron assembly biological_process 6.53e-02 1.73e-15 Reactome Chylomicron assembly Transport of small molecules 5.60e-02 1.06e-07 Reactome Scavenging by Class B Receptors Vesicle-mediated transport 5.55e-02 1.71e-12 GO positive regulation of cholesterol esterification biological_process 5.41e-02 4.44e-07 Reactome Diseases associated with visual transduction Disease 5.01e-02 4.44e-07 Reactome Retinoid cycle disease events Disease 4.91e-02 8.77e-05 Reactome Transport of fatty acids Transport of small molecules 4.60e-02 1.32e-17 GO high-density lipoprotein particle cellular_component 4.59e-02 1.85e-07 GO positive regulation of triglyceride catabolic process biological_process 2.73e-02 6.14e-09 GO phospholipid transporter activity molecular_function 2.13e-02 7.57e-12 GO phosphatidylcholine binding molecular_function 1.65e-02 1.71e-12 GO very-low-density lipoprotein particle remodeling biological_process 1.06e-02 3.03e-17 GO cholesterol efflux biological_process 8.31e-03 9.20e-06 GO cysteine-type endopeptidase inhibitor activity molecular_function 6.86e-03 5.94e-06 GO tissue regeneration biological_process 5.08e-03 7.48e-26 GO cellular protein metabolic process 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 lipid localization 0.00e+00 0.00e+00 lipid transport 0.00e+00 0.00e+00 regulation of plasma lipoprotein particle levels 0.00e+00 0.00e+00 phospholipid transport 0.00e+00 0.00e+00 lipoprotein metabolic process 0.00e+00 0.00e+00 cholesterol transport 0.00e+00 0.00e+00 sterol transport 0.00e+00 0.00e+00 reverse cholesterol transport 0.00e+00 0.00e+00 plasma lipoprotein particle remodeling 0.00e+00 0.00e+00 cholesterol efflux 0.00e+00 0.00e+00 high-density lipoprotein particle remodeling 0.00e+00 0.00e+00 very-low-density lipoprotein particle 0.00e+00 0.00e+00 chylomicron 0.00e+00 0.00e+00 high-density lipoprotein particle 0.00e+00 0.00e+00 plasma lipoprotein particle 0.00e+00 0.00e+00 protein-lipid complex 0.00e+00 0.00e+00 lipid transporter activity 0.00e+00 0.00e+00 lipid binding 7.74e-12 6.99e-09 cholesterol metabolic process 8.10e-12 7.31e-09 plasma lipoprotein particle assembly

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 0.00e+00 0.00e+00 LIPOPROTEIN METABOLISM 0.00e+00 0.00e+00 CHYLOMICRON MEDIATED LIPID TRANSPORT 0.00e+00 0.00e+00 LIPID DIGESTION MOBILIZATION AND TRANSPORT 0.00e+00 0.00e+00 AMYLOIDS 0.00e+00 0.00e+00 LIPOPROTEIN METABOLISM 0.00e+00 0.00e+00 LIPID DIGESTION MOBILIZATION AND TRANSPORT 0.00e+00 0.00e+00 AMYLOIDS 2.20e-12 6.49e-10 CHYLOMICRON MEDIATED LIPID TRANSPORT 2.73e-10 9.49e-08 HDL MEDIATED LIPID TRANSPORT 9.07e-10 2.22e-07 HDL MEDIATED LIPID TRANSPORT 1.42e-03 1.59e-01 PPARA ACTIVATES GENE EXPRESSION 2.81e-03 2.50e-01 PPARA ACTIVATES GENE EXPRESSION 8.40e-03 6.98e-01 FATTY ACID TRIACYLGLYCEROL AND KETONE BODY METABOLISM 1.87e-02 1.00e+00 FATTY ACID TRIACYLGLYCEROL AND KETONE BODY METABOLISM 2.28e-02 1.00e+00 PLATELET SENSITIZATION BY LDL 2.70e-02 1.00e+00 PLATELET SENSITIZATION BY LDL 2.96e-02 1.00e+00 CASPASE MEDIATED CLEAVAGE OF CYTOSKELETAL PROTEINS 3.55e-02 1.00e+00 CASPASE MEDIATED CLEAVAGE OF CYTOSKELETAL PROTEINS 3.89e-02 1.00e+00 ABCA TRANSPORTERS IN LIPID HOMEOSTASIS 3.90e-02 1.00e+00 ABCA TRANSPORTERS IN LIPID HOMEOSTASIS

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 2.07e-09 6.26e-05 abnormal cholesterol homeostasis 1.54e-06 1.19e-02 abnormal circulating cholesterol level 2.88e-06 1.97e-02 amyloidosis 3.80e-06 2.36e-02 abnormal retinol level 4.49e-06 2.69e-02 decreased circulating HDL cholesterol level 6.66e-05 1.72e-01 decreased circulating cholesterol level 7.03e-05 1.79e-01 decreased circulating VLDL cholesterol level 1.08e-04 2.39e-01 abnormal circulating HDL cholesterol level 2.17e-04 3.66e-01 increased circulating triglyceride level 2.18e-04 3.67e-01 increased circulating LDL cholesterol level 3.19e-04 4.68e-01 decreased cholesterol efflux 5.62e-04 6.51e-01 increased circulating VLDL cholesterol level 6.87e-04 7.28e-01 decreased circulating LDL cholesterol level 7.61e-04 7.67e-01 abnormal lipid homeostasis 8.92e-04 8.42e-01 increased liver cholesterol level 1.31e-03 1.00e+00 increased spleen white pulp amount 2.45e-03 1.00e+00 increased cerebral infarction size 2.46e-03 1.00e+00 impaired acrosome reaction 2.96e-03 1.00e+00 reduced male fertility 3.78e-03 1.00e+00 abnormal vascular wound healing

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

²FDR corrected p-value (Benjamini-Hochberg)