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Bioinformatics Advance Access published online on July 1, 2009
Bioinformatics, doi:10.1093/bioinformatics/btp414
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© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Affy Exon Tissues: Exon Levels in Normal Tissues in Human, Mouse, and Rat

Andrew A. Pohl 1, Charles W. Sugnet 2, Tyson A. Clark 2, Kayla Smith 1, Pauline A. Fujita 1 and Melissa S. Cline 3,*

1Center for Biomolecular Science & Engineering, University of California, Santa Cruz, CA 95064, USA
2Affymetrix, Inc., 3420 Central Expressway, Santa Clara, CA 95051, USA
3Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, CA 95064, USA

*To whom correspondence should be addressed. Dr. Melissa S. Cline, E-mail: cline{at}biology.ucsc.edu


  Abstract

Summary: Most genes in human, mouse, and rat produce more than one transcript isoform. The Affymetrix Exon Array is a tool for studying the many processes that regulate RNA production, with separate probesets measuring RNA levels at known and putative exons. For insights on how exons levels vary between normal tissues, we constructed the Affy Exon Tissues track from tissue data published by Affymetrix. This track reports exon probeset intensities as log ratios relative to median values across the dataset and renders them as colored heat maps, to yield quick visual identification of exons with intensities that vary between normal tissues.

Availability: Affy Exon Tissues track is freely available under the UCSC Genome Browser (http://genome.ucsc.edu/) for human (hg18), mouse (mm8 and mm9), and rat (rn4).

Contact: cline{at}biology.ucsc.edu

Associate Editor: Prof. David Rocke

Received on May 19, 2009; revised on June 26, 2009; accepted on June 29, 2009

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