ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing
Open Access
- 25 February 2010
- journal article
- software
- Published by Springer Science and Business Media LLC in Genome Biology
- Vol. 11 (2), R22-13
- https://doi.org/10.1186/gb-2010-11-2-r22
Abstract
Chromatin interaction analysis with paired-end tag sequencing (ChIA-PET) is a new technology to study genome-wide long-range chromatin interactions bound by protein factors. Here we present ChIA-PET Tool, a software package for automatic processing of ChIA-PET sequence data, including linker filtering, mapping tags to reference genomes, identifying protein binding sites and chromatin interactions, and displaying the results on a graphical genome browser. ChIA-PET Tool is fast, accurate, comprehensive, user-friendly, and open source (available at http://chiapet.gis.a-star.edu.sg).Keywords
This publication has 16 references indexed in Scilit:
- An oestrogen-receptor-α-bound human chromatin interactomeNature, 2009
- Insights from genomic profiling of transcription factorsNature Reviews Genetics, 2009
- Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analysesGenome Research, 2009
- ChIP‐based methods for the identification of long‐range chromatin interactionsJournal of Cellular Biochemistry, 2009
- Integration of External Signaling Pathways with the Core Transcriptional Network in Embryonic Stem CellsCell, 2008
- Paired-End Mapping Reveals Extensive Structural Variation in the Human GenomeScience, 2007
- Genome-Wide Mapping of in Vivo Protein-DNA InteractionsScience, 2007
- Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture–on-chip (4C)Nature Genetics, 2006
- Chromosome-Wide Mapping of Estrogen Receptor Binding Reveals Long-Range Regulation Requiring the Forkhead Protein FoxA1Cell, 2005
- Genome-Wide Location and Function of DNA Binding ProteinsScience, 2000