PLANdbAffy: probe-level annotation database for Affymetrix expression microarrays

      The files containing information about Affymetrix microarrays were downloaded from the official Affymetrix site. For this
analysis we selected three 3' Gene arrays, Affymetrix HG-U133 Plus 2.0, HG-U133A and HG-U133B, and two Exon&Gene
level arrays, Human Gene 1.0 and Human Exon 1.0.

      Probe sequences were mapped to the genome using Blat. We allowed alignments with no more than two mismatches and
required 40- and more nucleotide introns for potential exon-junction probes. The hits found "probe alignment regions" were
stored and subjected to further analysis.

      We annotated each probe alignment region using the mRNA and EST alignments provided by UCSC, considering only
the sequences that were present in UniGene (219 build) for corresponding genes.

      For each probe alignment region, we have calculated the number of mRNA and EST that either support (spliced_est_in,
unspliced_est_in, mrna_in fields) or do not support (spliced_est_out, mrna_out fields) occurrence of the probe alignment region
in an exon.

      To present the quality of a probe we divided all probes into four classes, and assigned a color to each class Green probes
(the best ones) are the probes meeting three conditions. First, the probe is aligned to the target gene without mismatches.
Second, there are no matches of the probe to other genes. Third, there are no perfect alignments of the probe to non-coding
regions. Unlike the green probes a yellow probe has a perfect match to uncoding region. The yellow probes still have a perfect
match to the target gene and no matches with other genes. The red probes are the probes that have a perfect match to the
target gene and at least one alignment to other genes with no more than one mismatch. Finally, a black probe is aligned to
the target gene with at least one mismatch.

      The textual part of the interface consists of probe information section, probe alignment section and transcription state
section. The probe information section has four fields presenting the probe name ("text"), the probe position on the chip ("X",
"Y", "inter pos") and the colour representation of the probe's quality status ("sts"). Each gene and each probe alignment
region are supported by the graphical part of the database interface. It is organized as custom tracks to UCSC genome browser,
that allows one to utilize all information that is offered by UCSC browser for the corresponding region.