CHiCP: A web-based tool for the integrative and interactive visualization of promoter capture Hi-C datasets

Bioinformatics

Volumn 32, Issue 16, 2016, Pages 2511-2513

  Schofield, E C ^a   Carver, T ^a   Achuthan, P ^a   Freire Pritchett, P ^b   Spivakov, M ^b   Todd, J A ^a   Burren, O S ^a  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^b BABRAHAM INSTITUTE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

CHROMOSOME; COMPUTER GRAPHICS; GENOME; GENOMICS; INTERNET; PROMOTER REGION; REGULATORY SEQUENCE; SOFTWARE;

CHROMOSOMES; COMPUTER GRAPHICS; GENOME; GENOMICS; INTERNET; PROMOTER REGIONS, GENETIC; REGULATORY ELEMENTS, TRANSCRIPTIONAL; SOFTWARE;

EID: 84983338572     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btw173     Document Type: Article

References (14)

1. An, J. et al. (2015) J-Circos: an interactive Circos Plotter. Bioinformatics, 31, 1463-1465.
2. Belton, J.M., et al. (2012) Hi-C: a comprehensive technique to capture the conformation of genomes. Methods, 58, 268-276.
3. Cairns, J. et al. (2015) CHiCAGO: robust detection of DNA looping interactions in capture Hi-C data. bioRxiv. doi:10.1101/028068.
4. Cunningham, F. et al. (2015) Ensembl 2015. Nucleic Acids Res., 43, D662-D669.
5. Franke, A. et al. (2010) Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci. Nat. Genet., 42, 1118-1125.
6. Krzywinski, M. et al. (2009) Circos: an information aesthetic for comparative genomics. Genome Res., 19, 1639-1645.
7. Laird, M.R. et al. (2015) GenomeD3Plot: a library for rich, interactive visualizations of genomic data in web applications. Bioinformatics, 31, 3348-3349.
8. Maurano, M.T. et al. (2012) Systematic localization of common disease-associated variation in regulatory DNA. Science, 337, 1190-1195.
9. Mifsud, B. et al. (2015) Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C. Nat. Genet., 47, 598-606.
10. Petkau, A. et al. (2010) Interactive microbial genome visualization with GView. Bioinformatics, 26, 3125-3126.
11. Roadmap Epigenomics et al. (2015) Integrative analysis of 111 reference human epigenomes. Nature, 518, 317-330.
12. Sahlen, P. et al. (2015) Genome-wide mapping of promoter-anchored interactions with close to single-enhancer resolution. Genome Biol., 16, 156.
13. Schoenfelder, S. et al. (2015) The pluripotent regulatory circuitry connecting promoters to their long-range interacting elements. Genome Res., 25, 582-597.
14. Zhou, X. et al. (2013) Exploring long-range genome interactions using the WashU Epigenome Browser. Nat. Methods, 10, 375-376.