Rxivist logo

Rxivist combines preprints from bioRxiv with data from Twitter to help you find the papers being discussed in your field. Currently indexing 57,529 bioRxiv papers from 264,889 authors.

Deciphering programs of transcriptional regulation by combined deconvolution of multiple omics layers

By Daniel Huebschmann, Nils Kurzawa, Sebastian Steinhauser, Philipp Rentzsch, Stephen Kraemer, Carolin Andresen, Jeongbin Park, Roland Eils, Matthias Schlesner, Carl Herrmann

Posted 08 Oct 2017
bioRxiv DOI: 10.1101/199547

Metazoans are crucially dependent on multiple layers of gene regulatory mechanisms which allow them to control gene expression across developmental stages, tissues and cell types. Multiple recent research consortia have aimed to generate comprehensive datasets to profile the activity of these cell type- and condition-specific regulatory landscapes across many different cell lines and primary cells. However, extraction of genes or regulatory elements specific to certain entities from these datasets remains challenging. We here propose a novel method based on non-negative matrix factorization for disentangling and associating huge multi-assay datasets including chromatin accessibility and gene expression data. Taking advantage of implementations of NMF algorithms in the GPU CUDA environment full datasets composed of tens of thousands of genes as well as hundreds of samples can be processed without the need for prior feature selection to reduce the input size. Applying this framework to multiple layers of genomic data derived from human blood cells we unravel mechanisms of regulation of cell type-specific expression in T-cells and monocytes.

Download data

  • Downloaded 1,176 times
  • Download rankings, all-time:
    • Site-wide: 4,937 out of 57,553
    • In genomics: 858 out of 4,033
  • Year to date:
    • Site-wide: 16,143 out of 57,553
  • Since beginning of last month:
    • Site-wide: 16,344 out of 57,553

Altmetric data


Downloads over time

Distribution of downloads per paper, site-wide


Sign up for the Rxivist weekly newsletter! (Click here for more details.)


News