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GenomeFlow: a comprehensive graphical tool for modeling and analyzing 3D genome structure
MOTIVATION: Three-dimensional (3D) genome organization plays important functional roles in cells. User-friendly tools for reconstructing 3D genome models from chromosomal conformation capturing data and analyzing them are needed for the study of 3D genome organization. RESULTS: We built a comprehens...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6477968/ https://www.ncbi.nlm.nih.gov/pubmed/30215673 http://dx.doi.org/10.1093/bioinformatics/bty802 |
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author | Trieu, Tuan Oluwadare, Oluwatosin Wopata, Julia Cheng, Jianlin |
author_facet | Trieu, Tuan Oluwadare, Oluwatosin Wopata, Julia Cheng, Jianlin |
author_sort | Trieu, Tuan |
collection | PubMed |
description | MOTIVATION: Three-dimensional (3D) genome organization plays important functional roles in cells. User-friendly tools for reconstructing 3D genome models from chromosomal conformation capturing data and analyzing them are needed for the study of 3D genome organization. RESULTS: We built a comprehensive graphical tool (GenomeFlow) to facilitate the entire process of modeling and analysis of 3D genome organization. This process includes the mapping of Hi-C data to one-dimensional (1D) reference genomes, the generation, normalization and visualization of two-dimensional (2D) chromosomal contact maps, the reconstruction and the visualization of the 3D models of chromosome and genome, the analysis of 3D models and the integration of these models with functional genomics data. This graphical tool is the first of its kind in reconstructing, storing, analyzing and annotating 3D genome models. It can reconstruct 3D genome models from Hi-C data and visualize them in real-time. This tool also allows users to overlay gene annotation, gene expression data and genome methylation data on top of 3D genome models. AVAILABILITY AND IMPLEMENTATION: The source code and user manual: https://github.com/jianlin-cheng/GenomeFlow. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. |
format | Online Article Text |
id | pubmed-6477968 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-64779682019-04-25 GenomeFlow: a comprehensive graphical tool for modeling and analyzing 3D genome structure Trieu, Tuan Oluwadare, Oluwatosin Wopata, Julia Cheng, Jianlin Bioinformatics Applications Notes MOTIVATION: Three-dimensional (3D) genome organization plays important functional roles in cells. User-friendly tools for reconstructing 3D genome models from chromosomal conformation capturing data and analyzing them are needed for the study of 3D genome organization. RESULTS: We built a comprehensive graphical tool (GenomeFlow) to facilitate the entire process of modeling and analysis of 3D genome organization. This process includes the mapping of Hi-C data to one-dimensional (1D) reference genomes, the generation, normalization and visualization of two-dimensional (2D) chromosomal contact maps, the reconstruction and the visualization of the 3D models of chromosome and genome, the analysis of 3D models and the integration of these models with functional genomics data. This graphical tool is the first of its kind in reconstructing, storing, analyzing and annotating 3D genome models. It can reconstruct 3D genome models from Hi-C data and visualize them in real-time. This tool also allows users to overlay gene annotation, gene expression data and genome methylation data on top of 3D genome models. AVAILABILITY AND IMPLEMENTATION: The source code and user manual: https://github.com/jianlin-cheng/GenomeFlow. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. Oxford University Press 2019-04-15 2018-09-12 /pmc/articles/PMC6477968/ /pubmed/30215673 http://dx.doi.org/10.1093/bioinformatics/bty802 Text en © The Author(s) 2018. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com |
spellingShingle | Applications Notes Trieu, Tuan Oluwadare, Oluwatosin Wopata, Julia Cheng, Jianlin GenomeFlow: a comprehensive graphical tool for modeling and analyzing 3D genome structure |
title | GenomeFlow: a comprehensive graphical tool for modeling and analyzing 3D genome structure |
title_full | GenomeFlow: a comprehensive graphical tool for modeling and analyzing 3D genome structure |
title_fullStr | GenomeFlow: a comprehensive graphical tool for modeling and analyzing 3D genome structure |
title_full_unstemmed | GenomeFlow: a comprehensive graphical tool for modeling and analyzing 3D genome structure |
title_short | GenomeFlow: a comprehensive graphical tool for modeling and analyzing 3D genome structure |
title_sort | genomeflow: a comprehensive graphical tool for modeling and analyzing 3d genome structure |
topic | Applications Notes |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6477968/ https://www.ncbi.nlm.nih.gov/pubmed/30215673 http://dx.doi.org/10.1093/bioinformatics/bty802 |
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