3D-GNOME: an integrated web service for structural modeling of the 3D genome

• Published in: Nucleic acids research Vol. 44; no. W1; pp. W288 - W293
• Main Authors: Szalaj, Przemyslaw, Michalski, Paul J, Wróblewski, Przemysław, Tang, Zhonghui, Kadlof, Michal, Mazzocco, Giovanni, Ruan, Yijun, Plewczynski, Dariusz
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 08.07.2016
• Subjects: Cell Line, Transformed; Chromosomes; Computer Graphics; Computer Simulation; Genome, Human; Humans; Imaging, Three-Dimensional - methods; Information Storage and Retrieval; Internet; Lymphocytes - metabolism; Lymphocytes - pathology; Models, Biological; User-Computer Interface; Web Server issue
• ISSN: 0305-1048; 1362-4962
• DOI: 10.1093/nar/gkw437

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/.