Departament of Bioengineering and Bioinformatics, MV Lomonosov Moscow State University, Vorbyevy Gory 1-73, Moscow 119992, Russia.
Nucleic Acids Res. 2010 Jan;38(Database issue):D726-30. doi: 10.1093/nar/gkp969. Epub 2009 Nov 11.
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.
标准的 Affymetrix 技术通过测量与 25 聚核苷酸探针组的 mRNA 杂交的强度来评估基因表达，并通过稳健的平均方法总结探针信号强度。然而，在许多情况下，探针的信号强度与基因表达不相关。这可能是由于探针与另一个基因的转录物杂交、探针映射到内含子、选择性剪接、单核苷酸多态性和其他原因。我们开发了一个数据库，PLANdbAffy（可在 http://affymetrix2.bioinf.fbb.msu.ru 获得），其中包含了来自五个 Affymetrix 表达微阵列的探针序列与人类基因组对齐的结果。我们已经确定了与正确定向的编码区转录本相匹配的探针。对于每个这样的探针对齐区域，我们确定了包含探针序列的 mRNA 和 EST 序列。在数据库接口的文本部分，我们总结了覆盖探针对齐区域的序列和位于其中的 SNPs 的数据。我们数据库接口的图形部分是作为 UCSC 基因组浏览器的自定义轨道实现的，这允许用户利用 UCSC 浏览器提供的所有数据。
