Sanchez-Graillet Olivia, Stalteri Maria A, Rowsell Joanna, Upton Graham J G, Harrison Andrew P
Departments of Mathematical and Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, United Kingdom.
J Integr Bioinform. 2010 Feb 19;7(2):442. doi: 10.2390/biecoll-jib-2010-114.
We have used large surveys of Affymetrix GeneChip data in the public domain to conduct a study of antisense expression across diverse conditions. We derive correlations between groups of probes which map uniquely to the same exon in the antisense direction. When there are no probes assigned to an exon in the sense direction we find that many of the antisense groups fail to detect a coherent block of transcription. We find that only a minority of these groups contain coherent blocks of antisense expression suggesting transcription. We also derive correlations between groups of probes which map uniquely to the same exon in both sense and antisense direction. In some of these cases the locations of sense probes overlap with the antisense probes, and the sense and antisense probe intensities are correlated with each other. This configuration suggests the existence of a Natural Antisense Transcript (NAT) pair. We find the majority of such NAT pairs detected by GeneChips are formed by a transcript of an established gene and either an EST or an mRNA. In order to determine the exact antisense regulatory mechanism indicated by the correlation of sense probes with antisense probes, a further investigation is necessary for every particular case of interest. However, the analysis of microarray data has proved to be a good method to reconfirm known NATs, discover new ones, as well as to notice possible problems in the annotation of antisense transcripts.
我们利用公共领域中大量的Affymetrix基因芯片数据进行了一项关于不同条件下反义表达的研究。我们推导了在反义方向上唯一映射到同一外显子的探针组之间的相关性。当没有探针在正义方向上被分配到一个外显子时，我们发现许多反义组未能检测到连贯的转录块。我们发现这些组中只有少数包含表明转录的连贯反义表达块。我们还推导了在正义和反义方向上都唯一映射到同一外显子的探针组之间的相关性。在某些情况下，正义探针的位置与反义探针重叠，并且正义和反义探针强度相互关联。这种配置表明存在天然反义转录本（NAT）对。我们发现基因芯片检测到的大多数此类NAT对是由一个已确立基因的转录本与一个EST或一个mRNA形成的。为了确定由正义探针与反义探针的相关性所表明的确切反义调控机制，对于每一个感兴趣的特定情况都需要进一步研究。然而，微阵列数据分析已被证明是一种重新确认已知NAT、发现新NAT以及注意反义转录本注释中可能存在问题的好方法。
