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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, accepted September 29 2009, published online 5 Oct 2009 pdf html

HNF4-specific site search:
High-throughput DNA binding analysis of HNF4a, RXRa and COUPTF2 reveals an HNF4-specific motif.
Fang B, Mane-Padros D, Bolotin E, Jiang T, Sladek FM.
paper submitted 2011.

Introduction

HNF4 Motif Finder is a web-based tool designed to identify potential HNF4alpha (H4) binding sites in any DNA sequence. There are two applicaitons. One is an exact match search using ~1400 unique sequences that are bound by human or rat HNF4a2/8 in vitro using Protein Binding Microarrays (PBMs). The other is a Support Vector Machine (SVM) algorithm trained on those PBM results. The SVM predicts more than 10,000 HNF4 binding sequences with approximately 90% accuracy. Since only a fraction of those sequences have been verified experimentally, we suggest refering to these sequences as potential HNF4 binding sequence, until verified experimentally. The PBM search is using only the sequences bound on the PBM as described in the Bolotin et al. 2009. The number of the sequence correlates to its relative binding affinity on the PBM. The SVM scores have been generated using SVM regression model trained on the PBM results and are predicting relative binding affinity of the sequences as described in Bolotin et al. 2009. Higher number indicates better predicted binding affinity.

Disclaimer

Please use HNF4 Motif Finder 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!

Acknowledgements

HNF4 Motif Finder was created by: Eugene Bolotin.

HNF4 Motif Finder uses SVM R package ksvm by Alexandros Karatzoglou

HNF4 Motif Finder is based upon the programs:
EMBOSS
BioPerl 1.4

Supporting information

Table S1A HNF4 motifs 1-71; 142-217. Includes literature references and motif sequences.

Table S1B HNF4 motifs 72-141.
These motifs were predicted using Markov model and verified by EMSA.

HNF4 motifs in proximity to annotated human genes. (Will be available soon).

HNF4 motifs Tab delimited HNF4 motifs.

PWM consensus Note we do not use consensus in our predictions.

Hepatology supplemental data Hepatology, Bolotin et al. 2010

Feedback

Suggestions on how to improve HNF4 Motif Finder are heartily welcomed! Please email ybolo001 at student.ucr.edu