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

Summary: Promoter capture Hi-C (PCHi-C) allows the genome-wide interrogation of physical interactions between distal DNA regulatory elements and gene promoters in multiple tissue contexts. Visual integration of the resultant chromosome interaction maps with other sources of genomic annotations can p...

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Detalles Bibliográficos
Autores principales: Schofield, E. C., Carver, T., Achuthan, P., Freire-Pritchett, P., Spivakov, M., Todd, J. A., Burren, O. S.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2016
Materias:
Applications Notes
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4978926/
https://www.ncbi.nlm.nih.gov/pubmed/27153610
http://dx.doi.org/10.1093/bioinformatics/btw173
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author Schofield, E. C.
Carver, T.
Achuthan, P.
Freire-Pritchett, P.
Spivakov, M.
Todd, J. A.
Burren, O. S.
author_facet Schofield, E. C.
Carver, T.
Achuthan, P.
Freire-Pritchett, P.
Spivakov, M.
Todd, J. A.
Burren, O. S.
author_sort Schofield, E. C.
collection PubMed
description Summary: Promoter capture Hi-C (PCHi-C) allows the genome-wide interrogation of physical interactions between distal DNA regulatory elements and gene promoters in multiple tissue contexts. Visual integration of the resultant chromosome interaction maps with other sources of genomic annotations can provide insight into underlying regulatory mechanisms. We have developed Capture HiC Plotter (CHiCP), a web-based tool that allows interactive exploration of PCHi-C interaction maps and integration with both public and user-defined genomic datasets. Availability and Implementation: CHiCP is freely accessible from www.chicp.org and supports most major HTML5 compliant web browsers. Full source code and installation instructions are available from http://github.com/D-I-L/django-chicp. Contact: ob219@cam.ac.uk
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spelling pubmed-49789262016-08-11 CHiCP: a web-based tool for the integrative and interactive visualization of promoter capture Hi-C datasets Schofield, E. C. Carver, T. Achuthan, P. Freire-Pritchett, P. Spivakov, M. Todd, J. A. Burren, O. S. Bioinformatics Applications Notes Summary: Promoter capture Hi-C (PCHi-C) allows the genome-wide interrogation of physical interactions between distal DNA regulatory elements and gene promoters in multiple tissue contexts. Visual integration of the resultant chromosome interaction maps with other sources of genomic annotations can provide insight into underlying regulatory mechanisms. We have developed Capture HiC Plotter (CHiCP), a web-based tool that allows interactive exploration of PCHi-C interaction maps and integration with both public and user-defined genomic datasets. Availability and Implementation: CHiCP is freely accessible from www.chicp.org and supports most major HTML5 compliant web browsers. Full source code and installation instructions are available from http://github.com/D-I-L/django-chicp. Contact: ob219@cam.ac.uk Oxford University Press 2016-08-15 2016-04-08 /pmc/articles/PMC4978926/ /pubmed/27153610 http://dx.doi.org/10.1093/bioinformatics/btw173 Text en © The Author 2016. Published by Oxford University Press. All rights reserved. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Applications Notes
Schofield, E. C.
Carver, T.
Achuthan, P.
Freire-Pritchett, P.
Spivakov, M.
Todd, J. A.
Burren, O. S.
CHiCP: a web-based tool for the integrative and interactive visualization of promoter capture Hi-C datasets
title CHiCP: a web-based tool for the integrative and interactive visualization of promoter capture Hi-C datasets
title_full CHiCP: a web-based tool for the integrative and interactive visualization of promoter capture Hi-C datasets
title_fullStr CHiCP: a web-based tool for the integrative and interactive visualization of promoter capture Hi-C datasets
title_full_unstemmed CHiCP: a web-based tool for the integrative and interactive visualization of promoter capture Hi-C datasets
title_short CHiCP: a web-based tool for the integrative and interactive visualization of promoter capture Hi-C datasets
title_sort chicp: a web-based tool for the integrative and interactive visualization of promoter capture hi-c datasets
topic Applications Notes
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4978926/
https://www.ncbi.nlm.nih.gov/pubmed/27153610
http://dx.doi.org/10.1093/bioinformatics/btw173
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