Gene-level differential analysis at transcript-level resolution

BioRxiv : the Preprint Server for Biology
Lynn YiLior Pachter

Abstract

Gene-level differential expression analysis based on RNA-Seq is more robust, powerful and biologically actionable than transcript-level differential analysis. However aggregation of transcript counts prior to analysis results can mask transcript-level dynamics. We demonstrate that aggregating the results of transcript-level analysis allow for gene-level analysis with transcript-level resolution. We also show that p-value aggregation methods, typically used for meta-analyses, greatly increase the sensitivity of gene-level differential analyses. Furthermore, such aggregation can be applied directly to transcript compatibility counts obtained during pseudoalignment, thereby allowing for rapid and accurate model-free differential testing. The methods are general, allowing for testing not only of genes but also of any groups of transcripts, and we showcase an example where we apply them to perturbation analysis of gene ontologies.

Related Concepts

Meta Analysis (Statistical Procedure)
Genes
Aggregation
Differential Diagnosis
Protein Aggregation, Pathological
Analysis
Transcript
Gene Expression Analysis
Gene Ontology
RNA

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