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

2016; Oxford University Press; Volume: 44; Issue: W1 Linguagem: Inglês

10.1093/nar/gkw437

1362-4962

Przemysław Szałaj, Paul J. Michalski, Przemysław Wróblewski, Zhonghui Tang, Michał Kadlof, Giovanni Mazzocco, Yijun Ruan, Dariusz Plewczyński,

RNA modifications and cancer

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.