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doi:10.22028/D291-29441
Title: | Combining transcription factor binding affinities with open-chromatin data for accurate gene expression prediction |
Author(s): | Schmidt, Florian Gasparoni, Nina Gasparoni, Gilles Gianmoena, Kathrin Cadenas, Cristina Polansky, Julia K. Ebert, Peter Nordström, Karl Barann, Matthias Sinha, Anupam Fröhler, Sebastian Xiong, Jieyi Dehghani Amirabad, Azim Behjati Ardakani, Fatemeh Hutter, Barbara Zipprich, Gideon Felder, Bärbel Eils, Jürgen Brors, Benedikt Chen, Wei Hengstler, Jan G. Hamann, Alf Lengauer, Thomas Rosenstiel, Philip Walter, Jörn Erik Schulz, Marcel H. |
Language: | English |
Title: | Nucleic acids research |
Volume: | 45 |
Issue: | 1 |
Startpage: | 54 |
Endpage: | 66 |
Publisher/Platform: | Oxford University Press |
Year of Publication: | 2017 |
Publikation type: | Journal Article |
Abstract: | The binding and contribution of transcription factors (TF) to cell specific gene expression is often deduced from open-chromatin measurements to avoid costly TF ChIP-seq assays. Thus, it is important to develop computational methods for accurate TF binding prediction in open-chromatin regions (OCRs). Here, we report a novel segmentation-based method, TEPIC, to predict TF binding by combining sets of OCRs with position weight matrices. TEPIC can be applied to various open-chromatin data, e.g. DNaseI-seq and NOMe-seq. Additionally, Histone-Marks (HMs) can be used to identify candidate TF binding sites. TEPIC computes TF affinities and uses open-chromatin/HM signal intensity as quantitative measures of TF binding strength. Using machine learning, we find low affinity binding sites to improve our ability to explain gene expression variability compared to the standard presence/absence classification of binding sites. Further, we show that both footprints and peaks capture essential TF binding events and lead to a good prediction performance. In our application, gene-based scores computed by TEPIC with one open-chromatin assay nearly reach the quality of several TF ChIP-seq data sets. Finally, these scores correctly predict known transcriptional regulators as illustrated by the application to novel DNaseI-seq and NOMe-seq data for primary human hepatocytes and CD4+ T-cells, respectively. |
DOI of the first publication: | 10.1093/nar/gkw1061 |
URL of the first publication: | https://academic.oup.com/nar/article/45/1/54/2605711 |
Link to this record: | hdl:20.500.11880/27896 http://dx.doi.org/10.22028/D291-29441 |
ISSN: | 1362-4962 0305-1048 |
Date of registration: | 25-Sep-2019 |
Faculty: | NT - Naturwissenschaftlich- Technische Fakultät |
Department: | NT - Biowissenschaften |
Professorship: | NT - Prof. Dr. Jörn Walter |
Collections: | SciDok - Der Wissenschaftsserver der Universität des Saarlandes |
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