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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...
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Formato: | Texto |
Lenguaje: | English |
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BioMed Central
2008
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2654044/ https://www.ncbi.nlm.nih.gov/pubmed/19077303 http://dx.doi.org/10.1186/1471-2105-9-533 |
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author | Krebs, Arnaud Frontini, Mattia Tora, Làszlò |
author_facet | Krebs, Arnaud Frontini, Mattia Tora, Làszlò |
author_sort | Krebs, Arnaud |
collection | PubMed |
description | 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 ENSEMBL). In addition, GPAT provides access to the expression status of the corresponding genes from either existing transcriptomic databases or from user generated expression data sets. Furthermore, GPAT allows the localisation of the genomic coordinates relative to the chromosome bands and the well characterised ENCODE regions. We successfully used GPAT to analyse ChIP on chip data and to identify genes functionally regulated by the TATA binding protein (TBP). CONCLUSION: GPAT provides a quick, convenient and flexible way to annotate large sets of genomic positions obtained after pre-analysis of ChIP-chip, ChIP-seq or other high throughput sequencing-based techniques. Through the different annotation data displayed, GPAT facilitates the interpretation of genome wide datasets for molecular biologists. |
format | Text |
id | pubmed-2654044 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2008 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-26540442009-03-11 GPAT: Retrieval of genomic annotation from large genomic position datasets Krebs, Arnaud Frontini, Mattia Tora, Làszlò BMC Bioinformatics Software 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 ENSEMBL). In addition, GPAT provides access to the expression status of the corresponding genes from either existing transcriptomic databases or from user generated expression data sets. Furthermore, GPAT allows the localisation of the genomic coordinates relative to the chromosome bands and the well characterised ENCODE regions. We successfully used GPAT to analyse ChIP on chip data and to identify genes functionally regulated by the TATA binding protein (TBP). CONCLUSION: GPAT provides a quick, convenient and flexible way to annotate large sets of genomic positions obtained after pre-analysis of ChIP-chip, ChIP-seq or other high throughput sequencing-based techniques. Through the different annotation data displayed, GPAT facilitates the interpretation of genome wide datasets for molecular biologists. BioMed Central 2008-12-15 /pmc/articles/PMC2654044/ /pubmed/19077303 http://dx.doi.org/10.1186/1471-2105-9-533 Text en Copyright © 2008 Krebs et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Software Krebs, Arnaud Frontini, Mattia Tora, Làszlò GPAT: Retrieval of genomic annotation from large genomic position datasets |
title | GPAT: Retrieval of genomic annotation from large genomic position datasets |
title_full | GPAT: Retrieval of genomic annotation from large genomic position datasets |
title_fullStr | GPAT: Retrieval of genomic annotation from large genomic position datasets |
title_full_unstemmed | GPAT: Retrieval of genomic annotation from large genomic position datasets |
title_short | GPAT: Retrieval of genomic annotation from large genomic position datasets |
title_sort | gpat: retrieval of genomic annotation from large genomic position datasets |
topic | Software |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2654044/ https://www.ncbi.nlm.nih.gov/pubmed/19077303 http://dx.doi.org/10.1186/1471-2105-9-533 |
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