The Exon GeneChip contains over one million probe sets designed to interrogate individual exons rather than the 3' ends of transcripts as in traditional GeneChips. Exons were derived from a variety of annotations that have been divided into the classes Core, Extended and Full.
Probe sets are colored by class with the Core probe sets being the darkest and the Full being the lightest color. Additionally, probe sets that do not overlap the exons of a transcript cluster, but fall inside of its introns, are considered bounded by that transcript cluster and are colored slightly lighter. Probe sets that overlap the coding portion of the Core class are colored slightly darker.
The microarray track using this probe set can be displayed by turning on the Affy Exon Tissue track.
The exons interrogated by the probe sets displayed in this track are from the Affymetrix Exon 1.0 GeneChip and were derived from a number of sources. In addition to the millions of cDNA sequences contributed to the GenBank, dbEst and RefSeq databases by individual labs and scientists, the following annotations were used:
Ensembl: Hubbard T, Barker D, Birney E, Cameron G, Chen Y, Clark L, Cox T, Cuff J, Curwen V, Down T et al.. The Ensembl genome database project. Nucleic Acids Research. 2002 Jan 1;30(1):38-41.
Exoniphy: Siepel, A., Haussler, D. Computational identification of evolutionarily conserved exons. Proc. 8th Int'l Conf. on Research in Computational Molecular Biology, 177-186 (2004).
Geneid Genes: Parra, G., Blanco, E., Guigo, R. Geneid in Drosophila. Genome Res. 10(4), 511-515 (2000).
Genscan Genes: Burge, C., Karlin, S. Prediction of Complete Gene Structures in Human Genomic DNA. J. Mol. Biol. 268(1), 78-94 (1997).
microRNA: Griffiths-Jones, S. The microRNA Registry. Nucl. Acids Res. 32, D109-D111 (2004).
MITOMAP: Brandon, M. C., Lott, M. T., Nguyen, K. C., Spolim, S., Navathe, S. B., Baldi, P. & Wallace, D. C. MITOMAP: a human mitochondrial genome database--2004 update Nucl. Acids Res. 33(Database Issue):D611-613 (2005).
RNA Genes: Lowe, T. M., Eddy, S. R. tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence. Nucleic Acids Res., 25(5), 955-964 (1997).
SGP Genes: Wiehe, T., Gebauer-Jung, S., Mitchell-Olds, T., Guigo, R. SGP-1: prediction and validation of homologous genes based on sequence alignments. Genome Res., 11(9), 1574-83 (2001).
Twinscan Genes: Korf, I., Flicek, P., Duan, D., Brent, M.R. Integrating genomic homology into gene structure prediction. Bioinformatics 17, S140-148 (2001).
Vega Genes and Pseudogenes: The HAVANA group, Wellcome Trust Sanger Institute.