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

Nucleic Acids Res. 2016 Jul 8;44(W1):W288-93. doi: 10.1093/nar/gkw437. Epub 2016 May 16.


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/.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • 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*