ArticleNucleic acids research2011
Comprehensive exon array data processing method for quantitative analysis of alternative spliced variants.
Article in Nucleic acids research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed, 37 citations in OpenAlex.
- Alternative splicing discriminates molecular subtypes and has prognostic impact in diffuse large B-cell lymphoma.Blood cancer journal · 2017Trial
- Deregulation of COMMD1 is associated with poor prognosis in diffuse large B-cell lymphoma.PloS one · 2014Trial
- Aberrant expression of CPSF1 promotes head and neck squamous cell carcinoma via regulating alternative splicing.PloS one · 2020Article
- Comparative evaluation of isoform-level gene expression estimation algorithms for RNA-seq and exon-array platforms.Briefings in bioinformatics · 2017Article
- A proteogenomic approach to understand splice isoform functions through sequence and expression-based computational modeling.Briefings in bioinformatics · 2016Article
- iGEMS: an integrated model for identification of alternative exon usage events.Nucleic acids research · 2016Article
- The cis and trans effects of the risk variants of coronary artery disease in the Chr9p21 region.BMC medical genomics · 2015Article
- Early maternal alcohol consumption alters hippocampal DNA methylation, gene expression and volume in a mouse model.PloS one · 2015Article
- Molecular characterization of subcutaneous panniculitis-like T-cell lymphoma reveals upregulation of immunosuppression- and autoimmunity-associated genes.Orphanet journal of rare diseases · 2014Article
- Incorporating alternative splicing and mRNA editing into the genetic analysis of complex traits.BioEssays : news and reviews in molecular, cellular and developmental biology · 2014Article
- puma 3.0: improved uncertainty propagation methods for gene and transcript expression analysis.BMC bioinformatics · 2013Article
- Functional profiling of precursor MicroRNAs identifies MicroRNAs essential for glioma proliferation.PloS one · 2013Article
- Netrin-4 promotes glioblastoma cell proliferation through integrin β4 signaling.Neoplasia (New York, N.Y.) · 2012Article
- Comparative analysis of algorithms for integration of copy number and expression data.Nature methods · 2012Article
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.