CHIPAS, Tool for ChipOnChip analysis

J. Pačes¹ and R. Ivánek¹

¹Istitute of Molecular Genetics, ASCR, Videnska 1083, 14220, Prague, Czech Republic

hpaces@img.cas.cz

Keywords: ChipOnChip, pattern search, microarray, transcription factor

Abstract

ChIP-on-chip, also known as genome-wide location analysis, is a technique for isolation and identification of nucleotide sequences occupied by specific DNA binding proteins in cells. These binding sites may indicate functions of various transcriptional regulators and help identify their target genes during animal development and disease progression. The identified binding sites may also be used as a basis for annotating functional elements in genomes. The types of functional elements that one can identify using ChIP-on-chip include promoters, enhancers, repressor and silencing elements, insulators, boundary elements, and sequences that control DNA replication.

The chip-on-chip technology can typically be used for identification of genes that respond to the transcription factor in study. We present here software CHIPAS (released under GPL2) that makes it possible to obtain a set of the best binding sites for given transcription factor together with the identification and location of its consensus binding nucleotide sequences. Application of this software is demonstrated in serching for protein-binding sites in the mouse PAX6 gene.