Comprehensive analysis of high-throughput screens with HiTSeekR

Markus List, Steffen Schmidt, Helle Christiansen, Marc Rehmsmeier, Qihua Tan, Jan Mollenhauer, Jan Baumbach
2016 Nucleic Acids Research  
High-throughput screening (HTS) is an indispens- able tool for drug (target) discovery that currently lacks user-friendly software tools for the robust identification of putative hits from HTS experiments and for the interpretation of these findings in the context of systems biology. We developed HiTSeekR as a one-stop solution for chemical compound screens, siRNA knock-down and CRISPR/Cas9 knock-out screens, as well as microRNA inhibitor and -mimics screens. We chose three use cases that
more » ... trate the potential of HiTSeekR to fully exploit HTS screening data in quite heterogeneous contexts to generate novel hypotheses for follow-up experiments: (i) a genome-wide RNAi screen to uncover modulators of TNF␣, (ii) a combined siRNA and miRNA mimics screen on vorinostat resistance and (iii) a small compound screen on KRAS synthetic lethality. HiTSeekR is publicly available at http://hitseekr.compbio.sdu. dk. It is the first approach to close the gap between raw data processing, network enrichment and wet lab target generation for various HTS screen types.
doi:10.1093/nar/gkw554 pmid:27330136 pmcid:PMC5001608 fatcat:5exuui7rinaqlob7yd3ppdcqv4