期刊
NUCLEIC ACIDS RESEARCH
卷 44, 期 W1, 页码 W288-W293出版社
OXFORD UNIV PRESS
DOI: 10.1093/nar/gkw437
关键词
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资金
- National Leading Research Centre in Bialystok
- European Union under the European Social Fund
- Polish National Science Centre [2014/15/B/ST6/05082, 2013/09/B/NZ2/00121]
- European Cooperation in Science and Technology action [COST BM1405, COST BM1408]
- Director Innovation Fund from Jackson Laboratory
- NCI [R01 CA186714]
- Roux family as a Florine Roux Endowed Chair and Professor in Genomics and Computational Biology
Recent advances in high-throughput chromosome conformation capture (3C) technology, such as HiC and ChIA-PET, have demonstrated the importance of 3D genome organization in development, cell differentiation and transcriptional regulation. There is now a widespread need for computational tools to generate and analyze 3D structural models from 3C data. Here we introduce our 3D GeNOme Modeling Engine (3D-GNOME), a web service which generates 3D structures from 3C data and provides tools to visually inspect and annotate the resulting structures, in addition to a variety of statistical plots and heatmaps which characterize the selected genomic region. Users submit a bedpe (paired-end BED format) file containing the locations and strengths of long range contact points, and 3D-GNOME simulates the structure and provides a convenient user interface for further analysis. Alternatively, a user may generate structures using published ChIA-PET data for the GM12878 cell line by simply specifying a genomic region of interest. 3D-GNOME is freely available at http://3dgnome.cent.uw.edu.pl/.
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