PPRE Search Tool

PPAR response element (PPRE) search tool 

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Submitted by DR. ALAN PREM KUMAR (Ph.D.) :: Nuclear Receptors, ROS and Cancer Biology :: National University Medical Institutes :: Yong Loo Lin School of Medicine :: National University of Singapore::Clinical Research Center, MD11,  #B1-07, 10 Medical Drive, Singapore 117597 :: 65-6516 4446 (DID) :: 65-6773 5461 (Fax)   

PPRESearch is the first web program to search for PPRE elements online in the promoter region of any gene of interest. PPRESearch is developed very carefully, taking into consideration all the important parameters that are required for PPAR binding for better accuracy in searching the PPREs. The special features which make PPRESearch unique and accurate in PPRE prediction are as follows. PPRESearch searches for the PPRE repeats from the PPRE database. PPREs in the database are collected from the literature and which were shown to be experimentally validated through in vitro or in vivo binding assays. The PPRE isoform specificity, binding efficiency, pubmed id and their experimental validation assay type (in vitro or in vivo) for each PPRE as reported in the literatures are also included in the database and are displayed in output, PPRESearch allows the user to set threshold binding efficiency when searching for PPRE elements in a gene. In addition user could also search for PPREs with few mismatches from their PPRE consensus. For better user experience and understanding the PPRESearch displays the predicted promoter gene region with the mismatch nucleotide bases from its consensus in bold letters and outputs the start position of the gene promoter region. The information on PPRE isoform specificity and its corresponding binding strength helps to user to understand the PPAR isoform that can bind to it and preferences of PPARs. This program is available for public use at http://www.classicrus.com/PPRE/ 


References

1. Venkatachalam G, Sakharkar MK, Kumar AP, Clement MV. PPRESearch: Peroxisome Proliferator Activator Element Search Database. International Journal of Integrative Biology 2009, 8(1), 37-42.


2. Venkatachalam G,  Kumar AP, Loo SY, Pervaiz S, Clement MV, Sakharkar MK. Computational identification and experimental validation of PPRE motifs in NHE1 and MnSOD genes of Human. BMC Genomics 2009, 10(Suppl 3):S5.