Mapping of probesets from Affymetrix chips HG-U133A 2.0, HG-U133 Plus 2.0, and GNF1B
(GNF1H; Su et al. 2004) to catalog loci. The
following file contains a partial list of probesets which map to ZNF loci. The list
was generated using a selection strategy designed to identify probesets that report only on single ZNF
loci. This is of particular importance given the evolutionary history of this gene family.
The selection strategy employed errs on the side of caution and may potentially eliminate probesets which
legitimately report on single loci. In brief, the individual probe sequences from each chip were
BLASTed against the complete genomic sequences for all non-pseudogene catalog loci (using the
Representative Model's sequence). BLAST was performed with
sequence filtering turned off and with a lenient expect score cutoff of 0.1. The raw blast data was then
analyzed in the following fashion to pick out a subset of "favorable" probesets.
First, all raw blast data where the alignment length was < 20 were discarded. Then, probesets with the following
properties were kept:
A. There were at least 10 alignments to a target locus where those alignments were
better than 20/25.
B. The ratio of the # of alignments to the target locus over the total # of alignments to all loci was > 0.8.
(If the probeset sequences aligned to the target locus and no other loci, the ratio would equal 1. If the
probeset had only a few alignments to loci other than the target locus, the ratio would still be high.
But if the probeset had lots of alignments to another locus or a few alignments to lots of other loci,
the ratio would be low and the probeset excluded.)
From this initial "favorable" list of probesets, the final list was generated by identifying probesets where
all the member probe sequences perfectly aligned to the same target locus (and only to that target locus).
To be clear, some probe sequences from a probeset in this list may also align imperfectly to additional loci
(but most will not because of the methodology for generating the initial "favorable" probeset list).