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.

This web service provides individualized 3D models of genomic structures for all 2,504 samples from the 1000 Genomes Project phase 3 SV release. Enter an ID of a sample and choose a genomic region of interest at the New request page to obtain a 3D model of the region for this particular individual. The models are built at the resolution of individual chromatin loops and visualize alterations emerging in genomic structures after introduction of SVs. You can also upload to the service your own interaction data in bedpe (paired-end BED) format together with bed or vcf file containing SVs to visualize structures formed by the submitted long-range contacts and altered by the provided SVs. 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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The method was described and used in:
Michal Sadowski, Agnieszka Kraft, Przemyslaw Szalaj, Michal Wlasnowolski, Zhonghui Tang, Yijun Ruan, Dariusz Plewczynski.
Spatial chromatin architecture alteration by structural variations in human genomes at population scale.
bioRxiv 266981, 2018. https://www.biorxiv.org/content/early/2018/09/14/266981

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