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Knapp, B.* ; Rebhan, I.* ; Kumar, A.* ; Matula, P.* ; Kiani, N.A.* ; Binder, M.* ; Erfle, H.* ; Rohr, K.B.* ; Eils, R.* ; Bartenschlager, R.* ; Kaderali, L.*

Normalizing for individual cell population context in the analysis of high-content cellular screens.

BMC Bioinformatics 12:485 (2011)
Verlagsversion DOI
Open Access Gold
BACKGROUND: High-content, high-throughput RNA interference (RNAi) offers unprecedented possibilities to elucidate gene function and involvement in biological processes. Microscopy based screening allows phenotypic observations at the level of individual cells. It was recently shown that a cell's population context significantly influences results. However, standard analysis methods for cellular screens do not currently take individual cell data into account unless this is important for the phenotype of interest, i.e. when studying cell morphology. RESULTS: We present a method that normalizes and statistically scores microscopy based RNAi screens, exploiting individual cell information of hundreds of cells per knockdown. Each cell's individual population context is employed in normalization. We present results on two infection screens for hepatitis C and dengue virus, both showing considerable effects on observed phenotypes due to population context. In addition, we show on a non-virus screen that these effects can be found also in RNAi data in the absence of any virus. Using our approach to normalize against these effects we achieve improved performance in comparison to an analysis without this normalization and hit scoring strategy. Furthermore, our approach results in the identification of considerably more significantly enriched pathways in hepatitis C virus replication than using a standard analysis approach. CONCLUSIONS: Using a cell-based analysis and normalization for population context, we achieve improved sensitivity and specificity not only on a individual protein level, but especially also on a pathway level. This leads to the identification of new host dependency factors of the hepatitis C and dengue viruses and higher reproducibility of results.
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Publikationstyp Artikel: Journalartikel
Dokumenttyp Wissenschaftlicher Artikel
ISSN (print) / ISBN 1471-2105
e-ISSN 1471-2105
Zeitschrift BMC Bioinformatics
Quellenangaben Band: 12, Heft: , Seiten: , Artikelnummer: 485 Supplement: ,
Verlag BioMed Central
Begutachtungsstatus Peer reviewed