3D-GNOME: an integrated web service for structural modeling of the 3D genome
Przemyslaw Szalaj , Przemysław Piotr Michalski , Przemysław Wróblewski , Zhonghui Tang , Michał Kadlof , Giovanni Mazzocco , Yijun Ruan , Dariusz Plewczyński
Recent advances in high-throughput chromosome conformation capture (3C) technology, such as Hi-C 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/.
|Journal series||Nucleic Acids Research, ISSN 0305-1048, e-ISSN 1362-4962|
|Score|| = 40.0, 09-06-2020, ArticleFromJournal|
= 40.0, 09-06-2020, ArticleFromJournal
|Publication indicators||= 17; = 12; : 2016 = 2.657; : 2016 = 10.162 (2) - 2016=9.338 (5)|
* presented citation count is obtained through Internet information analysis and it is close to the number calculated by the Publish or Perish system.