3D-GNOME 2.0 - 3D chromatin organization web service

3D genome organization plays a critical role in its functioning. Alterations of this organization caused by structural variants (SVs) may lead to changes in gene transcription or even to disease. The recent advent of Chromosome Conformation Capture (3C) based techniques such as ChIA-PET and Hi-C allows us to investigate genome spatial organization. The rising volume of sequencing data in turn enables highly accurate identification of structural variation. Combination of those two sources of information can reveal mechanisms of genome regulation. By means of either creating a contact map (or heatmap) representing the frequency of interactions between pairs of genomic loci, or by identifying a set of strong, confident interactions.

This web service allows for creating 3D models of the genomic regions selected by the user and visualization of the alterations emerging in those regions after introduction of SVs provided by the user. Users can submit a bedpe (paired-end BED format) file containing the locations and strengths of long-range contact points together with bed or vcf file containing SVs or use data integrated into the service. The online tool visualizes chromatin contacts and 3D structures of the selected region with and without mutations for comparison. The visualizations are interactive and a simple explorative data analysis is provided by means of data statistics (for example the number of singletons and PET clusters contained in the region, or their average and maximal length), heatmaps and plots (interactions length distribution or the distribution of interacting loci across the selected region).

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