Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2009 Dec;4(2):131-5.
doi: 10.1186/1479-7364-4-2-131.

R and Bioconductor solutions for alternative splicing detection

Tzulip Phang  1
Affiliations

R and Bioconductor solutions for alternative splicing detection

Tzulip Phang. Hum Genomics. 2009 Dec.

Abstract

The detection of alternative splicing using microarray technology involves multiple computational steps: normalisation, filtering, detection and visualisation. In this review, these analyses are approached using the R and Bioconductor open-source computation solution. There is some discussion on how to integrate different Bioconductor packages, and some of their major features are demonstrated. In addition, the Xmap Genome Browser is incorporated as an integral part of the analysis and annotation workflow.

PubMed Disclaimer

Similar articles

See all similar articles

References

    1. Pio R, Montuenga LM. 'Alternative splicing in lung cancer'. J Thorac Oncol. 2009;4:674–678. doi: 10.1097/JTO.0b013e3181a520dc. - DOI - PubMed
    1. Johnson JM, Castle J, Garrett-Engele P, Kan Z. et al.'Genome-wide survey of human alternative pre-mRNA splicing with exon junction microarrays'. Science. 2003;302:2141–2144. doi: 10.1126/science.1090100. - DOI - PubMed
    1. Wang GS, Cooper TA. 'Splicing in disease: Disruption of the splicing code and the decoding machinery'. Nat Rev Genet. 2007;8:749–761. doi: 10.1038/nrg2164. - DOI - PubMed
    1. Black DL. 'Mechanisms of alternative pre-messenger RNA splicing'. Ann Rev Biochem. 2003;72:291–336. doi: 10.1146/annurev.biochem.72.121801.161720. - DOI - PubMed
    1. Affymetrix_Inc. 'Affymetrix White Papers: Exon Probeset Annotations and Transcript Cluster Grouping v1.0'. 2005. http://www.affymetrix.com/support/technical/whitepapers.affx (accessed October 2009)

LinkOut - more resources