Schema for Affy Exon Array - Affymetrix Human Exon Array Probes and Probesets
  Database: hg19    Primary Table: affyExonProbeFree    Row Count: 55,727   Data last updated: 2011-03-08
Format description: Browser extensible data
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 591smallint(5) unsigned range Indexing field to speed chromosome range queries.
chrom chr1varchar(255) values Reference sequence chromosome or scaffold
chromStart 875016int(10) unsigned range Start position in chromosome
chromEnd 875040int(10) unsigned range End position in chromosome
name 4054639_4054636varchar(255) values Name of item
score 0int(10) unsigned range Optional score, nominal range 0-1000
strand -char(1) values + or -
thickStart 875016int(10) unsigned range Start of where display should be thick (start codon)
thickEnd 875040int(10) unsigned range End of where display should be thick (stop codon)
reserved 10027008int(10) unsigned range Used as itemRgb as of 2004-11-22
blockCount 1int(10) unsigned range Number of blocks

Sample Rows
 
binchromchromStartchromEndnamescorestrandthickStartthickEndreservedblockCount
591chr18750168750404054639_40546360-875016875040100270081
591chr18751178751414054639_40546360-875117875141100270081
591chr18751348751584054639_40546360-875134875158100270081
591chr18751488751724054639_40546360-875148875172100270081
591chr18789478789714054639_40546380-878947878971100270081
591chr18790318790554054639_40546380-879031879055100270081
591chr18790948791184054639_40546380-879094879118100270081
591chr18791688791924054639_40546380-879168879192100270081
594chr1119023811902622315660_23156610+11902381190262100270081
594chr1119061211906362315660_23156610+11906121190636100270081

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

Affy Exon Array (affyExonArray) Track Description
 

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.