PENTACON data

Data set Repository

An extensive, annotated BII repository of large-scale data sets relevant to the NSAID response, including data sets published by the PENTACON consortium and by others.

Curated information about the genes involved in the arachidonic acid pathway

PENTACON curators compiled lists of human genes involved in the Arachidonic Acid Pathway (AAP) and related networks based on the expertise of PENTACON researchers, as well as curated information from external resources including KEGG, Reactome, and GO. The genes were ranked as "Gold Standard", "Likely" or "Predicted" to be involved in the Arachidonic Acid or related pathways according to available experimental evidence. Specific gene curation was then performed by PENTACON curators based on information available in UniProt, BRENDA, BindingDB and the literature. The manually curated information, including chemicals, tissue specificity and disease involvement, was captured using standardized ontology terms. All of the curated information is available from the PENTACON Curated Data Resource (CDR), as well as from this PENTACON Data page. More information on how to navigate the PENTACON Curated Data Resource and details about the curation are provided in the Help Document. For additional questions, please contact pentacon@genomics.princeton.edu .

Production files include:

AAP_genelist_20141013_production.txt and README: Core list of genes involved in the Arachidonic Acid Pathway (AAP); ranked as Gold Standard (Direct), Likely (Indirect), or Predicted.
Curation_AAP_Homo-sapiens_All_Topics_20160907_production.txt: Curation of AAP genes with various curation topics including tissue and disease association.
Curation_AAP_Homo-sapiens_IVM_20160907_production.txt: Compilation of isoforms, sequence variants, and mutagenesis sites for the AAP genes.
Curation_AAP_Homo-sapiens_Kinetics_20170630_production.txt: Kinetics details (Km, Vmax, chemicals) for AAP gene products.
Curation_AAP_Homo-sapiens_Readme_20160907_production.txt: README for all Curation AAP files.
Curation_BP_Homo-sapiens_All_Topics_20160907_production.txt: Curation of BP genes with various curation topics including tissue and disease association.
Curation_BP_Homo-sapiens_IVM_20160907_production.txt: Compilation of isoforms, sequence variants, and mutagenesis sites for the BP genes.
Curation_BP_Homo-sapiens_Kinetics_20141013_production.txt: Kinetics details (Km, Vmax, chemicals) for BP gene products.
Curation_BP_Homo-sapiens_Readme_20160907_production.txt: README for all Curation BP files.
Curation_AAE_Homo-sapiens_All_Topics_20160907_production.txt: Curation of AAE genes with various curation topics including tissue and disease association.
Curation_AAE_Homo-sapiens_IVM_20160907_production.txt: Compilation of isoforms, sequence variants, and mutagenesis sites for the AAE genes.
Curation_AAE_Homo-sapiens_Kinetics_20141013_production.txt: Kinetics details (Km, Vmax, chemicals) for AAE gene products.
Curation_AAE_Homo-sapiens_Readme_20160907_production.txt: README for all Curation AAE files.
Curation_AAP_Mus-musculus_All_Topics_20140421_production.txt and README.
Curation_AAP_Rattus-norvegicus_All_Topics_20140421_production.txt and README.
BP_AAE_genelist_20141013_production.txt and README: List of genes related to the Arachidonic Acid Pathway (AAP) with a focus on Blood Pressure (BP) Regulation. Initial curation pass is still in progress.

The following files are available as archived or preliminary/pre-release versions at this time:

Keyword_genelist_20130725_preliminary.txt and README: Gene list compiled by relevant keyword searches in UniProt and GeneGo. Genes are distinct from those provided in other gene lists. Used in preliminary analyses and is now archived.
AAP_related_pathways_list_20130725_preliminary.txt and README: Preliminary set of pathways identified as related to the NSAID project for PENTACON; pathway links obtained from various external resources. Initial curation pass is still in progress.
Protein_DNA_Interactions_20141009_preliminary.txt and README: Preliminary set of protein-DNA interactions relevant to the transcriptional regulation of genes involved in the AAP. Initial curation pass is still in progress.

Curated Protein and Genetic Interactions

Protein and genetic interactions have also been curated for components of the Arachidonic Acid Pathway (AAP) as well as for any genes related to the AAP and blood pressure regulation. These molecular interactions are curated via the BioGRID database (http://www.thebiogrid.org) and are automatically added to the publicly available BioGRID monthly releases. The BIoGRID TAB 2.0 format is described here.

The following files are available:

Human-Mouse-Rat-Fish-Yeast: Orthologs and Analogs

PENTACON curators identified mouse, rat, fish, and yeast orthologs and analogs of human arachidonic acid pathway genes using P-POD version 4 (Heinicke et al 2007) and IMP (Wong et al 2012). Orthologs were based on P-POD's OrthoMCL analysis when possible or, when the human gene was not assigned to an OrthoMCL family, on P-POD's MultiParanoid analysis. Functional analogs were obtained from IMP using a cutoff of p web table or can be downloaded as tab-delimited files (Orthologs and Analogs file, the README, and the evidence code file).