Affy Exon Probes Track Settings
 
Affymetrix Exon Array 1.0: Probesets   (Affy Exon)

This track is part of a parent called 'Affy Exon'. To show other tracks of this parent, go to the Affy Exon configuration page.

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Data last updated: 2009-01-28

Description

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.

  • Core: RefSeq transcripts, full-length GenBank mRNAs
  • Extended: dbEst alignments, Ensembl annotations, syntenic mRNA from human, rat and mouse, microRNA annotations, MITOMAP annotations, Vega genes, Vega pseudogenes
  • Full: Geneid genes, Genscan genes, Genscan Subopt, Exoniphy, RNA genes, SGP genes, Twinscan genes

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.

Credits and References

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 Res. 2002 Jan 1;30(1):38-41. PMID: 11752248; PMC: PMC99161

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, Guigó R. GeneID in Drosophila. Genome Res. 2000 Apr;10(4):511-5. PMID: 10779490; PMC: PMC310871

Genscan Genes: Burge C, Karlin S. Prediction of complete gene structures in human genomic DNA. J Mol Biol. 1997 Apr 25;268(1):78-94. PMID: 9149143

microRNA: Griffiths-Jones S. The microRNA Registry. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D109-11. PMID: 14681370; PMC: PMC308757

MITOMAP: Kogelnik AM, Lott MT, Brown MD, Navathe SB, Wallace DC. MITOMAP: a human mitochondrial genome database. Nucleic Acids Res. 1996 Jan 1;24(1):177-9. PMID: 8594574; PMC: PMC145607

RNA Genes: Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 1997 Mar 1;25(5):955-64. PMID: 9023104; PMC: PMC146525

SGP Genes: Wiehe T, Gebauer-Jung S, Mitchell-Olds T, Guigó R. SGP-1: prediction and validation of homologous genes based on sequence alignments. Genome Res. 2001 Sep;11(9):1574-83. PMID: 11544202; PMC: PMC311140

Twinscan Genes: Korf I, Flicek P, Duan D, Brent MR. Integrating genomic homology into gene structure prediction. Bioinformatics. 2001;17 Suppl 1:S140-8. PMID: 11473003

Vega Genes and Pseudogenes: The HAVANA group, Wellcome Trust Sanger Institute.