Abstract:
:Alternative splicing of pre-mRNA generates protein diversity. Dysfunction of splicing machinery and expression of specific transcripts has been linked to cancer progression and drug response. Exon microarray technology enables genome-wide quantification of expression levels of the majority of exons and facilitates the discovery of alternative splicing events. Analysis of exon array data is more challenging than the analysis of gene expression data and there is a need for reliable quantification of exons and alternatively spliced variants. We introduce a novel, computationally efficient methodology, Multiple Exon Array Preprocessing (MEAP), for exon array data pre-processing, analysis and visualization. We compared MEAP with existing pre-processing methods, and validation of six exons and two alternatively spliced variants with qPCR corroborated MEAP expression estimates. Analysis of exon array data from head and neck squamous cell carcinoma (HNSCC) cell lines revealed several transcripts associated with 11q13 amplification, which is related with decreased survival and metastasis in HNSCC patients. Our results demonstrate that MEAP produces reliable expression values at exon, alternatively spliced variant and gene levels, which allows generating novel experimentally testable predictions.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Chen P,Lepikhova T,Hu Y,Monni O,Hautaniemi Sdoi
10.1093/nar/gkr513subject
Has Abstractpub_date
2011-10-01 00:00:00pages
e123issue
18eissn
0305-1048issn
1362-4962pii
gkr513journal_volume
39pub_type
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journal_title:Nucleic acids research
pub_type: 杂志文章
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更新日期:2017-01-25 00:00:00
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journal_title:Nucleic acids research
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journal_title:Nucleic acids research
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journal_title:Nucleic acids research
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