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Extracting quantitative genetic interaction phenotypes from matrix combinatorial RNAi.

Authors :
Axelsson E
Sandmann T
Horn T
Boutros M
Huber W
Fischer B
Source :
BMC bioinformatics [BMC Bioinformatics] 2011 Aug 17; Vol. 12, pp. 342. Date of Electronic Publication: 2011 Aug 17.
Publication Year :
2011

Abstract

Background: Systematic measurement of genetic interactions by combinatorial RNAi (co-RNAi) is a powerful tool for mapping functional modules and discovering components. It also provides insights into the role of epistasis on the way from genotype to phenotype. The interpretation of co-RNAi data requires computational and statistical analysis in order to detect interactions reliably and sensitively.<br />Results: We present a comprehensive approach to the analysis of univariate phenotype measurements, such as cell growth. The method is based on a quantitative model and is demonstrated on two example Drosophila cell culture data sets. We discuss adjustments for technical variability, data quality assessment, model parameter fitting and fit diagnostics, choice of scale, and assessment of statistical significance.<br />Conclusions: As a result, we obtain quantitative genetic interactions and interaction networks reflecting known biological relationships between target genes. The reliable extraction of presence, absence, and strength of interactions provides insights into molecular mechanisms.

Details

Language :
English
ISSN :
1471-2105
Volume :
12
Database :
MEDLINE
Journal :
BMC bioinformatics
Publication Type :
Academic Journal
Accession number :
21849035
Full Text :
https://doi.org/10.1186/1471-2105-12-342