LncDIFF: a novel quasi-likelihood method for differential expression analysis of non-coding RNA.

ABSTRACT:

Background

Long non-coding RNA (lncRNA) expression data have been increasingly used in finding diagnostic and prognostic biomarkers in cancer studies. Existing differential analysis tools for RNA sequencing do not effectively accommodate low abundant genes, as commonly observed in lncRNAs.

Results

We investigated the statistical distribution of normalized counts for low expression genes in lncRNAs and mRNAs, and proposed a new tool lncDIFF based on the underlying distribution pattern to detect differentially expressed (DE) lncRNAs. lncDIFF adopts the generalized linear model with zero-inflated Exponential quasi-likelihood to estimate group effect on normalized counts, and employs the likelihood ratio test to detect differential expressed genes. The proposed method and tool a

SUBMITTER: Li Q 

PROVIDER: S-EPMC6604377 | biostudies-literature | 2019 Jul

REPOSITORIES: biostudies-literature