Comprehensive Analysis of Affymetrix Exon Arrays Using BioConductor

Why BioConductor? BioConductor [1] is a collection of open source software packages designed to support the analysis of biological data. BioConductor is written using the programming language R, which itself provides access to a wide range of tools for statistical analysis, data presentation, and visualization. BioConductor has more than 200 packages representing not only analytical tools but also data and annotation. It has a highly active international developers' community. For those unfamiliar with R and BioConductor, numerous books and tutorials exist (see, for example, [2–4]), and there are also very active e-mail mailing lists for both.

• Publication year

  2008

• Venue

  PLoS Comput. Biol.

• Publication date

  2008-02-01

• Fields of study

  Biology, Medicine, Computer Science

• Identifiers
  DOI 10.1371/journal.pcbi.0040006PMID 18463711PMCID 2323405
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• An annotation infrastructure for the analysis and interpretation of Affymetrix exon array data

  2007cited by this paper
• Transcript-based redefinition of grouped oligonucleotide probe sets using AceView: High-resolution annotation for microarrays

  2007cited by this paper
• High correspondence between Affymetrix exon and standard expression arrays.

  2007cited by this paper
• Bioinformatics and Computational Biology Solutions Using R and Bioconductor

  2007cited by this paper
• Discovery of tissue-specific exons using comprehensive human exon microarrays

  2007cited by this paper
• Exon arrays provide accurate assessments of gene expression

  2007cited by this paper
• Bioinformatics and Computational Biology Solutions Using R and Bioconductor

  2006cited by this paper
• Alternative splicing and differential gene expression in colon cancer detected by a whole genome exon array

  2006cited by this paper
• The affymetrix GeneChip platform: an overview.

  2006cited by this paper
• Unbalanced alternative splicing and its significance in cancer

  2006cited by this paper
• Ensembl 2007

  2006cited by this paper
• Gene Signal Estimates

  2005cited by this paper
• Guide to Probe Logarithmic Intensity Error ( PLIER ) Estimation

  2005cited by this paper
• Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data

  2005cited by this paper
• Exon Array Background Correction

  2005cited by this paper
• Bioconductor: open software development for computational biology and bioinformatics

  2004cited by this paper
• Genome-Wide Survey of Human Alternative Pre-mRNA Splicing with Exon Junction Microarrays

  2003cited by this paper
• Summaries of Affymetrix GeneChip probe level data.

  2003cited by this paper
• Pre-mRNA splicing and human disease.

  2003cited by this paper
• Analysis of high density expression microarrays with signed-rank call algorithms

  2002cited by this paper
• A genomic view of alternative splicing

  2002cited by this paper
• Adjusting for multiple testing--when and how?

  2001cited by this paper
• S Programming

  2000cited by this paper
• A Core Lab Case Study : Exon Array Challenges and Opportunities

  year unknowncited by this paper

• Integrated analysis of long non-coding RNAs and mRNA profiles reveals potential sex-dependent biomarkers of bevacizumab/erlotinib response in advanced lung cancer

  2020cites this paper
• Discovery of a transcriptomic core of genes shared in 8 primary retinoblastoma with a novel detection score analysis

  2020cites this paper
• Mitochondrial PITRM1 peptidase loss-of-function in childhood cerebellar atrophy

  2018cites this paper
• Development of a simple artificial intelligence method to accurately subtype breast cancers based on gene expression barcodes

  2018cites this paper
• 24h-gene variation effect of combined bevacizumab/erlotinib in advanced non-squamous non-small cell lung cancer using exon array blood profiling

  2017cites this paper
• Association of multiparametric MRI quantitative imaging features with prostate cancer gene expression in MRI-targeted prostate biopsies

  2016cites this paper
• Improving cross‐study prediction through addon batch effect adjustment or addon normalization

  2016cites this paper
• Boulesteix Improving cross-study prediction through addon batch effect adjustment and addon normalization

  2016cites this paper
• In vivo profiling reveals immunomodulatory effects of sorafenib and dacarbazine on melanoma

  2015cites this paper
• Epigenome-Guided Analysis of the Transcriptome of Plaque Macrophages during Atherosclerosis Regression Reveals Activation of the Wnt Signaling Pathway

  2014cites this paper
• Estimating differential expression from multiple indicators

  2014cites this paper
• Transcriptome and Epigenome Applications for Coronary Heart Disease Research

  2014cites this paper
• Identification of therapeutic targets in acute myeloid leukaemia expressing the mutant RAS oncogene

  2014cites this paper
• The function of TCF4 in Pitt-Hopkins syndrome and schizophrenia

  2013cites this paper
• The impact of quantile and rank normalization procedures on the testing power of gene differential expression analysis

  2013cites this paper
• Whole-transcriptome profiling of thyroid nodules identifies expression-based signatures for accurate thyroid cancer diagnosis.

  2013cites this paper
• Combining clinicopathological and molecular pathway signatures for improving clinical decisions through an understanding of colorectal cancer biology

  2013cites this paper
• Spatio-temporal approach to transport dynamics in the mammalian brain ventricular system.

  2013cites this paper
• Transcriptome wide characterization of target sites and alternative splicing regulation mediated by RBM10

  2013cites this paper
• DiffSplice: the genome-wide detection of differential splicing events with RNA-seq

  2012cites this paper
• Mammary gland selective excision of c-jun identifies its role in mRNA splicing.

  2012cites this paper
• Transcriptome variation in breast cancer

  2012cites this paper
• Genomic studies of the normal and malignant neural crest

  2012cites this paper
• Microfluidic microarray for pathogenic DNA Analysis: single-base-pair-mismatch discrimination, and modeling/simulation of centrifugal flows and dynamic hybridization

  2012cites this paper
• Novel schizophrenia risk genesand gene expression

  2012influential citation
• Comparative transcriptome and network biology analyses demonstrate antiproliferative and hyperapoptotic phenotypes in human keratoconus corneas.

  2011cites this paper
• Knowledge-Driven, Data-Assisted Integrative Pathway Analytics

  2011cites this paper
• Novel analysis approaches to context-dependent molecular networks

  2011cites this paper
• U1 adaptors result in reduction of multiple pre-mRNA species principally by sequestering U1snRNP

  2011cites this paper
• Comprehensive exon array data processing method for quantitative analysis of alternative spliced variants

  2011cites this paper
• rnaSeqMap: a Bioconductor package for RNA sequencing data exploration

  2011cites this paper
• Spatiotemporal transcriptome of the human brain

  2011cites this paper
• Molecular Biology Primer for Neurosurgeons

  2011cites this paper
• U 1 adaptors result in reduction of multiple pre-mRNA species principally by sequestering U 1 snRNP

  2011cites this paper
• Microarray bioinformatics.

  2011cites this paper
• Analysis of Affymetrix Exon Arrays

  2010cites this paper
• System-Level Analysis of Neuroblastoma Tumor–Initiating Cells Implicates AURKB as a Novel Drug Target for Neuroblastoma

  2010cites this paper
• Tourette syndrome: Gene expression as a tool to discover drug targets

  2010cites this paper
• The comparison of different pre- and post-analysis filters for determination of exon-level alternative splicing events using Affymetrix arrays.

  2010cites this paper
• AltAnalyze and DomainGraph: analyzing and visualizing exon expression data

  2010cites this paper
• Multidimensional Gene Set Analysis of Genomic Data

  2010cites this paper
• Exon Array Analysis using re-defined probe sets results in reliable identification of alternatively spliced genes in non-small cell lung cancer

  2010cites this paper
• Probe-level estimation improves the detection of differential splicing in Affymetrix exon array studies

  2009cites this paper
• Evaluation of Microarray Preprocessing Algorithms Based on Concordance with RT-PCR in Clinical Samples

  2009cites this paper
• Real-time DNA microarrays: reality check.

  2009cites this paper
• Gene expression profiling in the rhesus macaque: methodology, annotation and data interpretation.

  2009cites this paper
• Exon Array Analysis of Head and Neck Cancers Identifies a Hypoxia Related Splice Variant of LAMA3 Associated with a Poor Prognosis

  2009cites this paper
• Overestimation of alternative splicing caused by variable probe characteristics in exon arrays

  2009cites this paper
• Performances de la puce exon et son application dans l’analyse de l’épissage alternatif associé à la métastase du cancer de sein

  2009cites this paper
• Bioconductor Annual Report 2008

  2008cites this paper