Comparison of Affymetrix Gene Array with the Exon Array shows potential application for detection of transcript isoform variation

Table 1 Summary of overlap between Alt Events and probes by isoform type

Isoform Type	Total Alt Events	# of Events Overlapped by Gene Array	# of Events Overlapped by Exon Array
Alternative Polyadenylation Site	1,684	41 (2.4%)	229 (13.6%)
Alternative 5' Intron Splice Site	3,634	1,433 (39.4%)	2,088 (57.5%)
Alternative 3' Intron Splice Site	5,332	1,806 (33.9%)	2,558 (48.0%)
Alternative Promoter Site	19,409	7,577 (39.0%)	14,826 (76.4%)
Overlapping Exon	9,876	4,535 (45.9%)	8,149 (82.5%)
Cassette Exon	24,511	16,670 (68.0%)	21,840 (89.1%)
Minor Introns*	182	22 (12.1%)	144 (79.1%)
Retained Intron	5,150	2,095 (40.7%)	4,549 (88.3%)
Strange Intron Ends**	4,281	233 (5.4%)	1,246 (29.1%)
Total	74,059	34,412 (46%)	55,629 (75%)

* Intron with AT/AC ends rather than the usual GT/AG
** Intron with ends that are not GT/AG, GC/AG or AT/AC
The total number of Alt Events sharing overlap with Gene Array and Exon Array platforms is summarized in the table above. Results are categorized based on isoform type. Definitions of each isoform category can be found in the Alt Events track description page in the UCSC Genome Browser http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=knownAlt. Note that some Alt Events overlap each other and are considered independently.

ISSN: 1471-2164