New Algorithm for Analysis of Off-target Effects in siRNA Screens

Karol Kozak, Sandra Kaestner, Thomas Wild, Andreas Vonderheit, Benjamin Misselwitz, Ulrike Kutay, Gabor Csucs


The occurrence of RNAi side effects called “off-target effects” is still a challenging aspect in the interpretation of data from large-scale RNA interference screens. To reduce off-target effects, improved algorithms have been developed for small interfering RNA (siRNA) design, but also chemical modifications of double stranded RNA molecules were introduced by the various commercial providers. To aid the analysis of large-scale screens, we present a new algorithm and tool for the prediction of potential off-target effects that can be applied to RNAi experimental data. Our approach provides different possibilities to search for homologies between individual siRNAs of cellular mRNAs. We demonstrate our approach on a ribosomal RNAi screening dataset.


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Paper Citation

in Harvard Style

Kozak K., Kaestner S., Wild T., Vonderheit A., Misselwitz B., Kutay U. and Csucs G. (2013). New Algorithm for Analysis of Off-target Effects in siRNA Screens . In Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2013) ISBN 978-989-8565-35-8, pages 253-260. DOI: 10.5220/0004185802530260

in Bibtex Style

author={Karol Kozak and Sandra Kaestner and Thomas Wild and Andreas Vonderheit and Benjamin Misselwitz and Ulrike Kutay and Gabor Csucs},
title={New Algorithm for Analysis of Off-target Effects in siRNA Screens},
booktitle={Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2013)},

in EndNote Style

JO - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2013)
TI - New Algorithm for Analysis of Off-target Effects in siRNA Screens
SN - 978-989-8565-35-8
AU - Kozak K.
AU - Kaestner S.
AU - Wild T.
AU - Vonderheit A.
AU - Misselwitz B.
AU - Kutay U.
AU - Csucs G.
PY - 2013
SP - 253
EP - 260
DO - 10.5220/0004185802530260