title: Alternative expression analysis by RNA sequencing.
abstract: In alternative expression analysis by sequencing (ALEXA-seq), we developed a method to analyze massively parallel RNA sequence data to catalog transcripts and assess differential and alternative expression of known and predicted mRNA isoforms in cells and tissues. As proof of principle, we used the approach to compare fluorouracil-resistant and -nonresistant human colorectal cancer cell lines. We assessed the sensitivity and specificity of the approach by comparison to exon tiling and splicing microarrays and validated the results with reverse transcription-PCR, quantitative PCR and Sanger sequencing. We 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. Alternative expression annotation databases, source code, a data viewer and other resources to facilitate analysis are available at http://www.alexaplatform.org/alexa_seq/.
authors.affiliation: Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, Canada.
authors.forename: Malachi
authors.initials: M
authors.lastname: Griffith
authors.forename: Obi L
authors.initials: OL
authors.lastname: Griffith
authors.forename: Jill
authors.initials: J
authors.lastname: Mwenifumbo
authors.forename: Rodrigo
authors.initials: R
authors.lastname: Goya
authors.forename: A Sorana
authors.initials: AS
authors.lastname: Morrissy
authors.forename: Ryan D
authors.initials: RD
authors.lastname: Morin
authors.forename: Richard
authors.initials: R
authors.lastname: Corbett
authors.forename: Michelle J
authors.initials: MJ
authors.lastname: Tang
authors.forename: Ying-Chen
authors.initials: YC
authors.lastname: Hou
authors.forename: Trevor J
authors.initials: TJ
authors.lastname: Pugh
authors.forename: Gordon
authors.initials: G
authors.lastname: Robertson
authors.forename: Suganthi
authors.initials: S
authors.lastname: Chittaranjan
authors.forename: Adrian
authors.initials: A
authors.lastname: Ally
authors.forename: Jennifer K
authors.initials: JK
authors.lastname: Asano
authors.forename: Susanna Y
authors.initials: SY
authors.lastname: Chan
authors.forename: Haiyan I
authors.initials: HI
authors.lastname: Li
authors.forename: Helen
authors.initials: H
authors.lastname: McDonald
authors.forename: Kevin
authors.initials: K
authors.lastname: Teague
authors.forename: Yongjun
authors.initials: Y
authors.lastname: Zhao
authors.forename: Thomas
authors.initials: T
authors.lastname: Zeng
authors.forename: Allen
authors.initials: A
authors.lastname: Delaney
authors.forename: Martin
authors.initials: M
authors.lastname: Hirst
authors.forename: Gregg B
authors.initials: GB
authors.lastname: Morin
authors.forename: Steven J M
authors.initials: SJ
authors.lastname: Jones
authors.forename: Isabella T
authors.initials: IT
authors.lastname: Tai
authors.forename: Marco A
authors.initials: MA
authors.lastname: Marra
mesh_terms: D017398:Alternative Splicing; D000964:Antimetabolites, Antineoplastic / Q000494:pharmacology; D045744:Cell Line, Tumor; D015179:Colorectal Neoplasms / Q000188:drug therapy / Q000235:genetics / Q000473:pathology; D030541:Databases, Genetic; D019008:Drug Resistance, Neoplasm / Q000235:genetics; D020224:Expressed Sequence Tags; D005472:Fluorouracil / Q000494:pharmacology; D015870:Gene Expression / Q000187:drug effects; D020869:Gene Expression Profiling; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis; D020033:Protein Isoforms; D012333:RNA, Messenger / Q000235:genetics*; D020133:Reverse Transcriptase Polymerase Chain Reaction; D016415:Sequence Alignment; D017423:Sequence Analysis, RNA / Q000379:methods*
chemical_list: D000964:Antimetabolites, Antineoplastic; D020033:Protein Isoforms; D012333:RNA, Messenger; D005472:Fluorouracil