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Simultaneous analysis of large-scale RNAi screens for pathogen entry
- Source :
- BMC genomics, BMC Genomics, 15, BMC Genomics (15), article 1162 (18 p.). (2014), BMC Genomics, BMC Genomics, 2014, 15, article 1162 (18 p.). ⟨10.1186/1471-2164/15/1162⟩, BMC Genomics, BioMed Central, 2014, 15, article 1162 (18 p.). ⟨10.1186/1471-2164/15/1162⟩
- Publication Year :
- 2014
- Publisher :
- BioMed Central, 2014.
-
Abstract
- Background Large-scale RNAi screening has become an important technology for identifying genes involved in biological processes of interest. However, the quality of large-scale RNAi screening is often deteriorated by off-targets effects. In order to find statistically significant effector genes for pathogen entry, we systematically analyzed entry pathways in human host cells for eight pathogens using image-based kinome-wide siRNA screens with siRNAs from three vendors. We propose a Parallel Mixed Model (PMM) approach that simultaneously analyzes several non-identical screens performed with the same RNAi libraries. Results We show that PMM gains statistical power for hit detection due to parallel screening. PMM allows incorporating siRNA weights that can be assigned according to available information on RNAi quality. Moreover, PMM is able to estimate a sharedness score that can be used to focus follow-up efforts on generic or specific gene regulators. By fitting a PMM model to our data, we found several novel hit genes for most of the pathogens studied. Conclusions Our results show parallel RNAi screening can improve the results of individual screens. This is currently particularly interesting when large-scale parallel datasets are becoming more and more publicly available. Our comprehensive siRNA dataset provides a public, freely available resource for further statistical and biological analyses in the high-content, high-throughput siRNA screening field.<br />BMC Genomics, 15<br />ISSN:1471-2164
- Subjects :
- Small interfering RNA
base de séquences
hit detection
[SDV]Life Sciences [q-bio]
arn i
Genomics
Computational biology
Biology
Proteomics
Cell Line
1311 Genetics
RNA interference
High-Throughput Screening Assays
Genetics
Humans
RNA, Small Interfering
Gene Library
Effector
high-throughput high-content RNAi screening
Scale (chemistry)
screening
Reproducibility of Results
pathogen entry
linear mixed model
10124 Institute of Molecular Life Sciences
ROC Curve
Host-Pathogen Interactions
High-throughput high-content RNAi screening
Pathogen entry
Linear mixed model
Hit detection
1305 Biotechnology
570 Life sciences
biology
RNA Interference
DNA microarray
Biotechnology
Research Article
Subjects
Details
- Language :
- English
- ISSN :
- 14712164
- Database :
- OpenAIRE
- Journal :
- BMC genomics, BMC Genomics, 15, BMC Genomics (15), article 1162 (18 p.). (2014), BMC Genomics, BMC Genomics, 2014, 15, article 1162 (18 p.). ⟨10.1186/1471-2164/15/1162⟩, BMC Genomics, BioMed Central, 2014, 15, article 1162 (18 p.). ⟨10.1186/1471-2164/15/1162⟩
- Accession number :
- edsair.doi.dedup.....9539cd22b9c8444577acf818184f83f5