Question about what a particular Affymetrix microarray probeset is detecting

[biznatch]

Sorry not a sequencing question exactly, but I thought this might still be a good place to ask (is there a better place to ask microarray questions?).

Most of the time if I get the target sequence for a probeset from the NetAffx website and then do a BLAT search the probeset aligns to the same strand as the transcript/gene it's detecting. For example, this one aligns to the "+" strand and detects the gene Cxcr2 which is also on the "+" strand:

>MOUSE430_2:1421734_AT
gcatggcatcattaccagagactgtggtatttgaattgatgcagcccctcctctacatta
cagggagaaagaggtcacgttcttcttagcagagccccccagagttttagaaccccctat
atggctgtctgacccccttcatcattggtatgcctactgatagagttgatccatcctaac
actgagaccccaaacactcttttctaagaagcacactttacaattacgtgagatctgcct
ctacccatgcagaacagttagcagtaaaggaagaggtggaggagtagaaaatggcaagtg
acaatgagaagtagaaaaagggaactcttcaccttaccagtagacgagtaccagagtccc
ctcacacaggaaatagca

This one aligns to the "-" strand and detects the gene Ntn1 which is also on the "-" strand:

>MOUSE430_2:1422987_AT
gtgaacatcatctccgtgtacaagcagggcacaagtcgtattcgccgtggtgaccagagt
ttgtggatccgctcacgagacatcgcctgcaagtgtcccaaaatcaagcccctcaagaag
tacttgctgttgggtaatgccgaggactcacctgaccagagtggcatcgtggcagacaag
agcagcctggtgatccagtggcgggacacatgggcacggcggctgcgcaagttccagcaa
cgggagaagaagggcaagtgcaagaaggcctagcgcggaggtggcgcgggctccaggagg
gcgggcagggcgctggcaaaggctggcagccttggacttggccgtcaggggttttttngg
gagggtgggggcggggcgaagtcgaagtggggcggggccctcagcggctccgccccagac
ccaccctcacacccctggctgcgctcttatgcgcatggcagaaagcaccctg

This is an example of a probeset I'm having a problem with:

>MOUSE430_2:1446891_AT
atcaactcctaccaatgttaccatgtaatttgataaaaatttgaatctttaactctgaaa
gtgacctggaagttaaaaacacgatgggggaataaacacagaaagtgggtgtctgtgagt
tcatcgtgctctacatagtgaaatcccaagacagcctaggctctggaaagagaccctatc
tggaaaaaagattcccaagcaaataaatgaaactacttttaaactgttaacaggatacac
ctcccagatgaaactattttgtagatttaagggagggaaaaaggctgtgatttatgagtt
aaaccactgtttcatacatggttttggatattctaacctaaatgattacaaacaacctag
aagagaagcaatctctttccttacctggctctggttaatagctgcatggttgccatggaa
tggagactgcctttctttatctcggtggtgacgactgctgtgtttgcttctctgcagttg
ctggcgtaattttgcaatctgaaa

According to Affymetrix it detects the gene Fam117b, except that the probeset aligns to the "-" strand while the gene is on the "+" strand. So is it really detecting the Fam117b gene (and if so, how?), or is it actually detecting an antisense transcript that happens to be transcribed from within the Fam117b gene but from the opposite strand? Are microarrays strand-specific?

[mastal]

The Affymetrix gene expression microarrays like the one you are using are strand specific.

The array will detect transcripts from whichever strand the probe sequences
(target sequence) come from.

If the gene is on the opposite strand to the probes, then it won't be detected by the array.

Most of the probesets on the array will be annotated accurately, however,
in cases where the annotation is based on a UniGene cluster, or where genes from different strands are close together, say at the 3' ends, then the annotation for the probeset can be problematic.