GPAT: Retrieval of genomic annotation from large genomic position datasets

Background: Recent genome wide transcription factor binding site or chromatin modification mapping analysis techniques, such as chromatin immunoprecipitation (ChIP) linked to DNA microarray analysis (ChIP on chip) or ChIP coupled to high throughput sequencing (ChIP-seq), generate tremendous amounts of genomic location data in the form of one-dimensional series of signals. After pre-analysis of these data (signal pre-clearing, relevant binding site detection), biologists need to search for the biological relevance of the detected genomic positions representing transcription regulation or chromatin modification events. Results: To address this problem, we have developed a Genomic Position Annotation Tool (GPAT) with a simple web interface that allows the rapid and systematic labelling of thousands of genomic positions with several types of annotations. GPAT automatically extracts gene annotation information around the submitted positions from different public databases (Refseq or ENSEMB...

• Type: Journal
• Year: 2008
• Where: BMCBI
• Authors: Arnaud Krebs, Mattia Frontini, Làszlò Tora
• Keywords: BMCBI 2008, Chip, Chromatin Modification, Genomic Positions