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?
What is the situation with CYP1A1 and CYP1A2? What region should be used?
3) Check whether probes for p53 (Swissprot: P53_HUMAN), p63 and p73 (P73_HUMAN) are available on the Affymetrix human 35K chip or the mouse 12K chip. Check whether there are sequence verified clones available from Research Genetics.
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? What could you do to resolve this issue?
[Answers]
1) Literature search with Pubmed:
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed
2) Sequence search & retrieval (SwissProt, Entrez)
http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?db=Nucleotide
3) BLAST searches at SIB
http://www.ch.embnet.org/software/aBLAST.html
Use specific subdatabase! Mind the ‘repsim‘ filter
4) Two-way sequence alignment