TF-Prioritizer: a java pipeline to prioritize condition-specific transcription factors
02:05 Share

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2022.10.19.512881v1?rss=1

Authors: Hoffmann, M., Trummer, N., Jankowski, J., Lee, H. K., Willruth, L.-L., Yuan, K., Lazareva, O., Baumgarten, N., Schmidt, F., Baumbach, J., Schulz, M. H., Blumenthal, D. B., Hennighausen, L., List, M.

Abstract: Background Eukaryotic gene expression is controlled by cis-regulatory elements (CREs) including promoters and enhancers which are bound by transcription factors (TFs). Differential expression of TFs and their putative binding sites on CREs cause tissue and developmental-specific transcriptional activity. Consolidating genomic data sets can offer further insights into the accessibility of CREs, TF activity, and thus gene regulation. However, the integration and analysis of multi-modal data sets are hampered by considerable technical challenges. While methods for highlighting differential TF activity from combined ChIP-seq and RNA-seq data exist, they do not offer good usability, have limited support for large-scale data processing, and provide only minimal functionality for visual result interpretation. Results We developed TF-Prioritizer, an automated java pipeline to prioritize condition-specific TFs derived from multi-modal data. TF-Prioritizer creates an interactive, feature-rich, and user-friendly web report of its results. To showcase the potential of TF-Prioritizer, we identified known active TFs (e.g., Stat5, Elf5, Nfib, Esr1), their target genes (e.g., milk proteins and cell-cycle genes), and newly classified lactating mammary gland TFs (e.g., Creb1, Arnt). Conclusion TF-Prioritizer accepts ChIP-seq and RNA-seq data, as input and suggests TFs with differential activity, thus offering an understanding of genome-wide gene regulation, potential pathogenesis, and therapeutic targets in biomedical research.

Copy rights belong to original authors. Visit the link for more info

Podcast created by Paper Player, LLC