Estimating the Expression of Transcript Isoforms from mRNA-Seq via Nonnegative Least Squares

Author

Kim, Hyunsoo ; Bi, Yingtao ; Davuluri, Ramana V.

Author_Institution

Center for Syst. & Comput. Biol., Wistar Inst., Philadelphia, PA, USA

fYear

2010

fDate

May 31 2010-June 3 2010

Firstpage

296

Lastpage

297

Abstract

mRNA-Seq is an emerging massive parallel sequencing based technology for identification and quantification of gene transcripts. Although gene level expression can easily be estimated from mRNA-Seq data, estimating the isoform level expression poses serious problems, and appropriate methods are required. In this paper, we introduce a mathematical method to estimate transcript isoform concentrations, i.e. transcript isoform expression estimation via nonnegative least squares (TIEE/NLS).

Keywords

bioinformatics; genetics; molecular biophysics; gene level expression; gene transcript identification; gene transcript quantification; mRNA-Seq; massive parallel sequencing based technology; nonnegative least squares; transcript isoform concentration; transcript isoform expression estimation; Bioinformatics; Biomedical engineering; Bismuth; Cancer; Cells (biology); Clustering algorithms; Computational biology; Data analysis; Genomics; Least squares approximation; mRNA-Seq; nonnegative least squares; transcript isoform; transcript isoform expression estimation;

fLanguage

English

Publisher

ieee

Conference_Titel

BioInformatics and BioEngineering (BIBE), 2010 IEEE International Conference on

Conference_Location

Philadelphia, PA

Print_ISBN

978-1-4244-7494-3

Type

conf

DOI

10.1109/BIBE.2010.61

Filename

5521668