## Methods

This track shows the genomic locations of the probesets and probes from the Affymetrix Exon array. This array was designed to interrogate every known and putative exon in the human genome. For the design of this array, Affymetrix compiled evidence of expression from sources including well-annotated genes such as RefSeq, genomic alignments of mRNA and EST sequences, gene predictions, exon predictions, and regions that are syntenic to conserved regions in related species. Using this evidence, Affymetrix designed a probeset for each known or putative exon. While some of these regions might never be transcribed, the goal is to obtain a comprehensive measurement of transcription in the human genome. In most cases, this array contains one probeset per exon. However, whenever this design-time evidence suggested that some exon had alternative splice sites, the exon was subdivided into two or more regions, and one probeset was designed for each region (where possible). The array contains no probesets for exons smaller than 25 nucleotides.

The exon array supports both gene-level and exon-level expression measurement. When the probesets for a single gene are analyzed together, it yields results for overall gene expression. When the probeset of each exon is contrasted against other exons in the same gene, it yields results for alternative splicing.

The probes and probesets on the exon array are divided into five levels or classes, depending mostly on the degree of design-time evidence.

- Core probes and probesets are supported by the most reliable evidence from RefSeq and full-length mRNA GenBank records containing complete CDS information.
- Extended probes and probesets are supported by other cDNA evidence beyond what is used to support core probe sets. Extended evidence comes from other Genbank mRNAs not annotated as full-length, EST sequences, ENSEMBL gene collections, syntenically mapped mRNA from Mouse, Rat, or Human, mitoMap mitochondrial genes, microRNA registry genes, vegaGene, and vegaPseudoGene records.
- Full probes and probesets are supported by computational gene prediction evidence only. They are supported by gene and exon prediction algorithms including GeneID, GenScan, GenScanSubOptimal, exoniphy, RNAGene, sgpGene and Twinscan.
- Free probes and probesets are supported by annotations which were merged such that no single annotation (or evidence) contains the probe setprobe sets that are supported by annotations which were merged such that no single annotation (or evidence) contains the probe set.
- Ambiguous probes and probesets cannot be assigned unambiguously to any single gene.

All probes and probesets have a two-part label, indicating the transcript cluster ID and probeset ID. The transcript cluster ID is a numeric representation of the gene interrogated by the probeset in question. All probes are labeled with the transcript cluster ID and probeset ID of whatever probeset they belong to.

## Credits

The data for this track were provided by Affymetrix. Further information on the Human Exon Array is available here.