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Statistical Tests for Detecting Differential RNA-Transcript Expression from Read Counts

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http://pubman.mpdl.mpg.de/cone/persons/resource/persons84969

Stegle,  O
Max Planck Institute for Biological Cybernetics, Max Planck Society;

http://pubman.mpdl.mpg.de/cone/persons/resource/persons83894

Drewe,  P
Department Empirical Inference, Max Planck Institute for Biological Cybernetics, Max Planck Society;

http://pubman.mpdl.mpg.de/cone/persons/resource/persons75313

Bohnert R, Borgwardt,  K
Max Planck Institute for Biological Cybernetics, Max Planck Society;

http://pubman.mpdl.mpg.de/cone/persons/resource/persons84153

Rätsch,  G
Department Empirical Inference, Max Planck Institute for Biological Cybernetics, Max Planck Society;

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Citation

Stegle, O., Drewe, P., Bohnert R, Borgwardt, K., & Rätsch, G. (2010). Statistical Tests for Detecting Differential RNA-Transcript Expression from Read Counts. Nature Precedings, 2010, 1-11. doi:10.1038/npre.2010.4437.1.


Cite as: http://hdl.handle.net/11858/00-001M-0000-0013-C02C-5
Abstract
As a fruit of the current revolution in sequencing technology, transcriptomes can now be analyzed at an unprecedented level of detail. These advances have been exploited for detecting differential expressed genes across biological samples and for quantifying the abundances of various RNA transcripts within one gene. However, explicit strategies for detecting the hidden differential abundances of RNA transcripts in biological samples have not been defined. In this work, we present two novel statistical tests to address this issue: a "gene structure sensitive" Poisson test for detecting differential expression when the transcript structure of the gene is known, and a kernel-based test called Maximum Mean Discrepancy when it is unknown. We analyzed the proposed approaches on simulated read data for two artificial samples as well as on factual reads generated by the Illumina Genome Analyzer for two C. elegans samples. Our analysis shows that the Poisson test identifies genes with differential transcript expression considerably better that previously proposed RNA transcript quantification approaches for this task. The MMD test is able to detect a large fraction (75) of such differential cases without the knowledge of the annotated transcripts. It is therefore well-suited to analyze RNA-Seq experiments when the genome annotations are incomplete or not available, where other approaches have to fail.