HNF4 Motif Finder-about

Nuclear Receptor Binding Site Scanner (NRBS Scanner)

Sladek Lab, University of California, Riverside Introduction Nuclear Receptor Binding Site Scanner (NRBS Scanner) is a web-based tool designed to identify potential nuclear receptor binding sites in any DNA sequence. There are two applications. The first application searches for binding sites for a given nuclear receptor using support vector machine (SVM) prediction. Binding sites are inferred by an SVM model trained on >1000 unique sequences that have been experimentally validated using Protein Binding Microarrays (PBMs). The sites with a probability of binding greater than 0.5 (maximum is 1.0) and their start positions in the user-provided DNA are shown. The second application searches for HNF4-specific binding sequences as defined in Fang et al. 2012. Both PBM-verified and SVM-predicted binding sites specific for HNF4 are given in the output. Sites present only in the SVM search should be referred to as potential binding sequences. Disclaimer Please use Nuclear Receptor Binding Site Scanner at your own risk. It is not a secure web site, the program is in development, so please let us know if you encounter any bugs. Enjoy! References PBM search, SVM search: Integrated Approach for the Identification of Human HNF4a Target Genes Using Protein Binding Microarrays. E. Bolotin, H. Liao, T.C. Ta, C. Yang, W. Hwang-Verslues, J.R. Evans, T. Jiang, and F.M. Sladek Hepatology Volume 51, Issue 2, Pages 642-653, 5 Oct 2009 HNF4-specific site search: Identification of a binding motif specific to HNF4 by comparative analysis of multiple nuclear receptors. Fang B, Mane-Padros D, Bolotin E, Jiang T, Sladek FM. Nucleic Acids Research. Epub 2012 Mar 01. PMID: 22383578. Acknowledgements Nuclear Receptor Binding Site Scanner was created by: Bin Fang. HNF4 Motif Finder uses SVM R package ksvm by Alexandros Karatzoglou Feedback Suggestions on how to improve Nuclear Receptor Binding Site Scanner are heartily welcomed! Please email bfang at ucr.edu