ENC Exon Array Super-track Settings
ENCODE Exon Array Tracks   (All Expression tracks)

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Duke Affy Exon  Affymetrix Exon Array from ENCODE/Duke  
UW Affy Exon  Affymetrix Exon Array from ENCODE/University of Washington  



These tracks display microarray data. Samples are hybridized to the Affymetrix Human Exon 1.0 GeneChip. In contrast to traditional microarrays, which are designed to measure overall gene expression, the Affymetrix exon arrays contain separate probesets for each exon. This allows large-scale measurement of alternative splicing, alternative polyadenylation, and alternative promoter usage. Additionally, analysis of the constitutive exons (those included in all transcripts) offer accurate measurement of overall gene expression levels. Further information on the design and content of exon arrays can be found here.

Display Conventions

Items on these tracks pertain to Affymetrix exon array probesets. For information regarding specific microarray probesets, turn on the Affy Exon Array track, which can be found in the "Expression" track group. These tracks are multi-view composite tracks that contains multiple data types (views). Each view within each track has separate display controls, as described here. Most ENCODE tracks contain multiple subtracks, corresponding to multiple experimental conditions. If a track contains a large number of subtracks, only some subtracks will be displayed by default. The user can select which subtracks are displayed via the display controls on the track details pages.


These data were generated and analyzed as part of the ENCODE project, a genome-wide consortium project with the aim of cataloging all functional elements in the human genome. This effort includes collecting a variety of data across related experimental conditions, to facilitate integrative analysis. Consequently, additional ENCODE tracks may contain data that is relevant to the data in these tracks.


Bemmo A, Benovoy D, Kwan T, Gaffney DJ, Jensen RV, Majewski J. Gene expression and isoform variation analysis using Affymetrix Exon Arrays. BMC Genomics. 2008 Nov 7;9:529.

Gardina PJ, Clark TA, Shimada B, Staples MK, Yang Q, Veitch J, Schweitzer A, Awad T, Sugnet C, Dee S, Davies C, Williams A, Turpaz Y. Alternative splicing and differential gene expression in colon cancer detected by a whole genome exon array. BMC Genomics. 2006 Dec 27;7:325.

Data Release Policy

Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column on the track configuration page and the download page. The full data release policy for ENCODE is available here.