We present a computational method to gain knowledge of the three-dimensional structure of the genome from ChIP-seq datasets. While not designed to detect contacts, the ChIP-seq protocol cross-links proteins with each other and with DNA. Consequently, genomic regions that interact with the protein binding-site via chromatin looping are co-immunoprecipitated and sequenced. This produces minor ChIP-seq signals around CTCF motif pairs at loop anchor regions. Together with genomic sequence features, these signals predict whether loop anchors interact or not. Our method, Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs (7C), is available as an R/Bioconductor package: http://bioconductor.org/packages/sevenC .
- Downloaded 1,431 times
- Download rankings, all-time:
- Site-wide: 6,758 out of 94,912
- In genomics: 1,048 out of 5,955
- Year to date:
- Site-wide: 50,559 out of 94,912
- Since beginning of last month:
- Site-wide: 85,579 out of 94,912
Downloads over time
Distribution of downloads per paper, site-wide
- 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!