生物芯片表达谱分析技术.ppt

For cDNA microarrays, multiple clones are also measured for a transcript to evaluate the consistency of microarray data. Ideally, such (these) multiple clones, especially the replicate ones, should have similar measurements. This sketch picture can help us understand the multiple clones designation in cDNA microarray. For each gene, specific cDNA clones are designed and spotted on cDNA microarray. Sometime, to evaluate the consistency of microarray data, multiple clones are also measured for the same unigene. These multiple clones fall into two categories: The first one are clones designed for different sequence segments of an Unigene. These clones target the same gene but different from each other (in sequence), they are called different clones, we refer them as DC for short in the following presentation. Basically, the DCs are mainly designed to account for the probe specificity of clones. And the second one are clones designed for an unique sequence segment of an Unigene, they are simply spotted on the microarray multiple-times. Because these clones are identical to each other, they are called replicate clones and RC for short. And the RCs are designed for controlling the systematic variance (random noise). To conclude, the multiple clones can be classified into two types: different sequence segments for a transcript (DC) and replicate sequence segment for a transcript (RC) Preparations: This table summarize clone annotation information of the gastric, liver and prostate cancer cDNA microarray datasets. Clones were annotated to Unigenes through the SOURCE database in Apr. 2008 and Oct. 2006 respectively. The numbers of DCs with UniGene decreased greatly in the all three cancer datasets when using the updated annotation data in 2008, and the numbers of RCs with UniGene decreased slightly. This phenomenon suggests the updating database indeed improve the reliability of annotation. This figure depicts the distributions of the correlations for the DC pairs in