Alternative expression analysis by sequencing (ALEXA-seq)
A method to analyze massively parallel RNA sequence data in order to catalog transcripts and assess differential and alternative expression of known and predicted mRNA isoforms in cells and tissues. The authors compared fluorouracil-resistant and -nonresistant human colorectal cancer cell lines and observed global disruption of splicing in fluorouracil-resistant cells characterized by expression of new mRNA isoforms resulting from exon skipping, alternative splice site usage and intron retention.
They assessed the sensitivity and specificity of ALEXA-seq by comparison to exon tiling and splicing microarrays and validated the results with reverse transcription–PCR, quantitative PCR and Sanger sequencing.
Alternative expression annotation databases, source code, a data viewer and other resources to facilitate analysis are available at http://www.alexaplatform.org/alexa_seq/.
Griffith M, Griffith OL, Mwenifumbo J, Goya R, Morrissy AS, Morin RD, Corbett R, Tang MJ, Hou YC, Pugh TJ, Robertson G, Chittaranjan S, Ally A, Asano JK, Chan SY, Li HI, McDonald H, Teague K, Zhao Y, Zeng T, Delaney A, Hirst M, Morin GB, Jones SJ, Tai IT, Marra MA. (2010) Alternative expression analysis by RNA sequencing. Nat Methods [Epub ahead of print]. [abstract]