FDM: a graph-based statistical method to detect differential transcription using RNA-seq data.

ABSTRACT:

Motivation

In eukaryotic cells, alternative splicing expands the diversity of RNA transcripts and plays an important role in tissue-specific differentiation, and can be misregulated in disease. To understand these processes, there is a great need for methods to detect differential transcription between samples. Our focus is on samples observed using short-read RNA sequencing (RNA-seq).

Methods

We characterize differential transcription between two samples as the difference in the relative abundance of the transcript isoforms present in the samples. The magnitude of differential transcription of a gene between two samples can be measured by the square root of the Jensen Shannon Divergence (JSD*) between the gene's transcript abundance vectors in each sample. We define a weigh

SUBMITTER: Singh D 

PROVIDER: S-EPMC3179659 | biostudies-literature | 2011 Oct

REPOSITORIES: biostudies-literature