Gene-level differential analysis at transcript-level resolution

Genome Biology
Lynn YiLior Pachter

Abstract

Compared to RNA-sequencing transcript differential analysis, gene-level differential expression analysis is more robust and experimentally actionable. However, the use of gene counts for statistical analysis can mask transcript-level dynamics. We demonstrate that 'analysis first, aggregation second,' where the p values derived from transcript analysis are aggregated to obtain gene-level results, increase sensitivity and accuracy. The method we propose can also be applied to transcript compatibility counts obtained from pseudoalignment of reads, which circumvents the need for quantification and is fast, accurate, and model-free. The method generalizes to various levels of biology and we showcase an application to gene ontologies.

References

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Citations

Nov 19, 2008·Nature Reviews. Genetics·Zhong WangMichael Snyder
Oct 29, 2010·Genome Biology·Simon Anders, Wolfgang Huber
Jun 23, 2012·Genome Research·Simon AndersWolfgang Huber
Dec 12, 2012·Nature Biotechnology·Cole TrapnellLior Pachter
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Related Concepts

Genes
Sequence Determinations, RNA
Aggregation
Analysis of Substances
Sequencing
Analysis
Gene Ontology Project
Transcript
Gene Expression Analysis
Gene Ontology

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