IMCD Proteome Database Edit

Citations: 0

z-index: 0

Basic information
Short name IMCD Proteome Database
Full name
Description This database of renal inner medullary collecting duct (IMCD) proteins is based on published protein mass spectrometry data from the NHLBI Epithelial Systems Biology Laboratory. All data are from IMCD cells freshly isolated from the renal medullas of rats.
URL https://hpcwebapps.cit.nih.gov/ESBL/Database/IMCD_Proteome_Database
Year founded
Last update & version
Accessibility Accessible
Contact information

The contact information is provided to facilitate update of database information, and it is curated based on the contact details in the database or the related publications. To ensure effective contact with database constructors, we give priority to the contact details in the database.

University/Institution National Heart, Lung and Blood Institute
Address Building 31, 31 Center Drive, Bethesda, MD 20892
City
Province/State
Country/Region United States
Contact name (PI/Team) Mark A. Knepper
Contact email (PI/Helpdesk) knep@helix.nih.gov
Data information
Data object
Data type
Database category
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Keyword
Publications
  • Sequence-based searching of custom proteome and transcriptome databases. [PMID: 30230259]
    Barbara Medvar, Abhijit Sarkar, Mark Knepper, Trairak Pisitkun

    A long-term goal in renal physiology is to understand the mechanisms involved in collecting duct function and regulation at a cellular and molecular level. The first step in modeling of these mechanisms, which can provide a guide to experimentation, is the generation of a list of model components. We have curated a list of proteins expressed in the rat renal inner medullary collecting duct (IMCD) from proteomic data from 18 different publications. The database has been posted as a public resource at https://hpcwebapps.cit.nih.gov/ESBL/Database/IMCD_Proteome_Database/. It includes 8956 different proteins. To search the IMCD Proteomic Database efficiently, we have created a Java-based program called curated database Basic Local Alignment Search Tool (cdbBLAST), which uses the NCBI BLAST kernel to search for specific amino acid sequences corresponding to proteins in the database. cdbBLAST reports information on the matched protein and identifies proteins in the database that have similar sequences. We have also adapted cdbBLAST to interrogate our previously published IMCD Transcriptome Database. We have made the cdbBLAST program available for use either as a web application or a downloadable .jar file at https://hpcwebapps.cit.nih.gov/ESBL/Database/cdbBLAST/. Database searching based on protein sequence removes ambiguities arising from the standard search method based on official gene symbols and allows the user efficient identification of related proteins that may fulfill the same functional roles.

    Physiol Rep 2018:6(18)

    0 Citations (from Europe PMC, 2019-06-08)

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The box plots depict Z-index distribution for all databases in Database Commons and for specific database category/categories. The red line indicates log2(Z-index) of IMCD Proteome Database.

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  • Created on: 2019-01-04
    • ***d@***c.cn [2019-01-07]
    • ***d@***c.cn [2019-01-04]

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