High-resolution interactions among regulatory elements are of crucial importance for the understanding of transcriptional regulation and the interpretation of disease mechanism. Hi-C technique allows the genome-wide detection of chromatin contacts. However, unless extremely deep sequencing is performed on a very large number of input cells, current Hi-C experiments do not have high enough resolution to resolve contacts among regulatory elements. Here, we develop DeepTACT, a bootstrapping deep learning model, to integrate genome sequences and chromatin accessibility data for the prediction of chromatin contacts among regulatory elements. In tests based on promoter capture Hi-C data, DeepTACT is seen to offer improved resolution over existing methods. DeepTACT analysis also identifies a class of hub promoters, which are active across cell lines, enriched in housekeeping genes, functionally related to fundamental biological processes, and capable of reflecting cell similarity. Finally, the utility of high-resolution chromatin contact information in the study of human diseases is illustrated by the association of IFNA2 and IFNA1 to coronary artery disease via an integrative analysis of GWAS data and high-resolution contacts inferred by DeepTACT.
- Downloaded 803 times
- Download rankings, all-time:
- Site-wide: 40,807
- In bioinformatics: 4,291
- Year to date:
- Site-wide: 132,897
- Since beginning of last month:
- Site-wide: 156,854
Downloads over time
Distribution of downloads per paper, site-wide
- 27 Nov 2020: The website and API now include results pulled from medRxiv as well as bioRxiv.
- 18 Dec 2019: We're pleased to announce PanLingua, a new tool that enables you to search for machine-translated bioRxiv preprints using more than 100 different languages.
- 21 May 2019: PLOS Biology has published a community page about Rxivist.org and its design.
- 10 May 2019: The paper analyzing the Rxivist dataset has been published at eLife.
- 1 Mar 2019: We now have summary statistics about bioRxiv downloads and submissions.
- 8 Feb 2019: Data from Altmetric is now available on the Rxivist details page for every preprint. Look for the "donut" under the download metrics.
- 30 Jan 2019: preLights has featured the Rxivist preprint and written about our findings.
- 22 Jan 2019: Nature just published an article about Rxivist and our data.
- 13 Jan 2019: The Rxivist preprint is live!