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Protocols

CPDB specifications

Information


Unique identifier OMICS_01903
Name CPDB
Alternative name ConsensusPathDB
Restrictions to use Academic or non-commercial use
Community driven No
Data access File download, Browse
User data submission Not allowed
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/ConsensusPathDB

Taxon


  • Primates
    • Homo sapiens

Additional information


Tutorial: http://cpdb.molgen.mpg.de/CPDB/tutorial

Publications for ConsensusPathDB

CPDB citations

 (79)
call_split

Blocking negative effects of senescence in human skin fibroblasts with a plant extract

2018
PMCID: 5895844
PMID: 29675264
DOI: 10.1038/s41514-018-0023-5
call_split See protocol

[…] ng for the keyword “secreted” (KW-0964) was done using DAVID v6.8. Pathway analysis was realised with Ingenuity pathway analysis software (Qiagen). Pathway enrichment analysis was performed employing ConsensusPathDB, by using the overrepresentation analysis tool. We searched against pathways in all databases with a minimal overlap and a p-value cut-off of 0.0001. […]

library_books

Network analysis of coronary artery disease risk genes elucidates disease mechanisms and druggable targets

2018
Sci Rep
PMCID: 5821758
PMID: 29467471
DOI: 10.1038/s41598-018-20721-6

[…] es). A score of 2 was assigned to each kinase and GPCR coding gene.Existing drugs targeting the gene product. The genes measured in the STAGE study and the proteins/genes they interact with (from the ConsensusPathDB) were checked with the HGNC Multi-symbol Checker. All unique gene names (including HGNC and non-HGNC converted names) were listed and checked for drug interactions in DGIdb v2.22 (Inte […]

library_books

In Silico Prediction of Chemical Toxicity for Drug Design Using Machine Learning Methods and Structural Alerts

2018
PMCID: 5826228
PMID: 29515993
DOI: 10.3389/fchem.2018.00030

[…] Chemical carcinogenesis is of increasing importance in drug discovery for its serious effect on human health. Most of the predictive models use Carcinogenic Potency Database (CPDB) as the data source, which contains more than 1,500 chemicals with their labels (carcinogen or non-carcinogen) according to their TD50 values (Gold et al., ). Recently several publications shared […]

library_books

Actionable perturbations of damage responses by TCL1/ATM and epigenetic lesions form the basis of T PLL

2018
Nat Commun
PMCID: 5814445
PMID: 29449575
DOI: 10.1038/s41467-017-02688-6

[…] between human and mouse were evaluated using Venny. Functional analyses of (differentially expressed) genes was carried out by Ingenuity Pathway Analysis (IPA, http://www.ingenuity.com/products/ipa), ConsensusPathDB (GSOA), Broad GSEA 2–2.2.1, and KEGG/GO enrichment from the R package STRINGdb, version 9_05.For identification of prognostic GEP signatures, GEPs of T-PLL cases with longest (>800 day […]

library_books

Unraveling endometriosis associated ovarian carcinomas using integrative proteomics

2018
F1000Res
PMCID: 5915760
PMID: 29721309
DOI: 10.5256/f1000research.15069.r31989

[…] ed values using singular value decomposition in order to find the principal components. Gene Ontology, the Protein Analysis Through Evolutionary Relationships (PANTHER) Classification System ( ), and ConsensusPathDB-human ( ) were utilized to retrieve additional annotations. […]

library_books

Asymmetric dimethylarginine (ADMA) is identified as a potential biomarker of insulin resistance in skeletal muscle

2018
Sci Rep
PMCID: 5794993
PMID: 29391561
DOI: 10.1038/s41598-018-20549-0

[…] ary Table ). To find common biological associations between insulin resistance and these metabolites, we performed both pathway analysis using the Pathway Studio and pathway enrichment analysis using ConsensusPathDB and KEGG pathway resources (Supplementary Fig. ). Sub-cellular network analysis demonstrated the metabolites shared biological significance underlying canonical signaling pathways such […]

Citations

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CPDB institution(s)
Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany; Department of Pathology and Cancer Center, Massachusetts General Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
CPDB funding source(s)
Supported in part by the European Commission under its 7th Framework Programme (HeCaToS 602156) and the Max Planck Society.

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