TY  - INPR
A1  - Hoffmann, Markus
A1  - Trummer, Nico
A1  - Jankowski, Jakub
A1  - Kyung Lee, Hye
A1  - Willruth, Lina-Liv
A1  - Lazareva, Olga
A1  - Yuan, Kevin
A1  - Baumgarten, Nina
A1  - Schmidt, Florian
A1  - Baumbach, Jan
A1  - Schulz, Marcel Holger
A1  - Blumenthal, David B.
A1  - Hennighausen, Lothar
A1  - List, Markus
T1  - TF-Prioritizer: a java pipeline to prioritize condition-specific transcription factors
T2  - bioRxiv
N2  - 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.
Y1  - 2022
UR  - http://publikationen.ub.uni-frankfurt.de/frontdoor/index/index/docId/75585
UR  - https://nbn-resolving.org/urn:nbn:de:hebis:30:3-755851
UR  - https://www.biorxiv.org/content/10.1101/2022.10.19.512881v1
IS  - 2022.10.19.512881 Version 1
ER  -