2) The cytochrome P450 family is very important for toxicological microarray analysis since most isoforms repond to different toxic compounds.
Is it possible to design a cDNA fragment (minimal size 200 bp) that would be able to separate CYP2A6 and CYP2A7? No, the 2 sequences are much too close to each other, they even seem to be variants rather than isoforms
What is the situation with CYP1A1 and CYP1A2? What region should be used? The 3'UTR region is sufficiently distinct and can be used (see ensembl)
4) Two (hypothetical) papers using different types of microarrays report very different results for the regulation of the thyroid receptor alpha (Swissprot: THA_HUMAN).
Can you think of a possible explanation? They used sequences specific to two splice-variants of the same protein.
What could you do to resolve this issue? Well it depends on the question you ask, but basically if you are not interested in one variant or the other, you could not use the results, because you are not able to sum the contribution of each variant. In a future experiment, it would be wise to use 3 fragments of the sequences. One common and two variant-specifics.