Nucleic Acids Research Advance Access published online on November 11, 2009
Nucleic Acids Research, doi:10.1093/nar/gkp969
Database Issue |
PLANdbAffy: probe-level annotation database for Affymetrix expression microarrays
1Departament of Bioengineering and Bioinformatics, M.V. Lomonosov Moscow State University, Vorbyevy Gory 1-73, Moscow 119992, Russia, 2Moscow Institute of Physics and Technology, Institutskii per. 9, Dolgoprudny, Moscow Region 141700, 3Gamaleya Institute of Epidemiology and Microbiology Russian Academy of Medical Sciences, Gamaleya Street, 18, Moscow 123098, 4Institute of Agricultural Biotechnology, Russian Academy of Agricultural Sciences, Timiryazevskay Street 42, Moscow 127550, Russia, 5Parascript LLC, Winchester Circle 6899, Ste. 200, Boulder, CO 80301, USA and 6A.N. Belozersky Institute of Physical and Chemical Biology, Moscow State University, Leninskie Gory 1-40, Moscow 119991, Russia
*To whom correspondence should be addressed. Tel: +7 495 939 14 59; Fax: +7 495 939 31 58; Email: ramil{at}bioinf.fbb.msu.ru
Received August 14, 2009. Revised October 12, 2009. Accepted October 14, 2009.
Standard Affymetrix technology evaluates gene expression by measuring the intensity of mRNA hybridization with a panel of the 25-mer oligonucleotide probes, and summarizing the probe signal intensities by a robust average method. However, in many cases, signal intensity of the probe does not correlate with gene expression. This could be due to the hybridization of the probe to a transcript of another gene, mapping of the probe to an intron, alternative splicing, single nucleotide polymorphisms and other reasons. We have developed a database, PLANdbAffy (available at http://affymetrix2.bioinf.fbb.msu.ru), that contains the results of the alignment of probe sequences from five Affymetrix expression microarrays to the human genome. We have determined the probes matching the transcript-coding regions in the correct orientation. For each such probe alignment region, we determined the mRNA and EST sequences that contain the probe sequence. In the textual part of the database interface we summarize the data on the sequences that cover the probe alignment region and SNPs that are located inside it. The graphical part of our database interface is implemented as custom tracks to the UCSC genome browser that allows one to utilize all the data that are offered by UCSC browser.
Present address: Ramil N. Nurtdinov, INSERM U563, Pole des Neurosciences, University of Toulouse, BP 3048, CHU Purpan, Toulouse 3, 31024, France.