《计算系统生物学导论》系统生物学导论-2012-2.pptVIP

The Introduction of ?Computational Systems Biology 计算系统生物学导论 Wang Dong Associate Professor? Email: wangdong@ems.hrbmu.edu.cn Life’s Complexity Pyramid 高通量生物信息检测与 “omics” Genomics（基因组） Gene identification charaterisation Static，but completely specified Transcriptomics（表达组） Expression profiles of mRNA Dynamic, context-dependent Proteomics（蛋白质组） functions interactions of proteins Dynamic， context-dependent Structural Genomics（结构组） Large scale structure determination Cellinomics（细胞组：代谢组，互作组） Metabolic Pathways Cell-cell interactions Pharmacogenomics（药物基因组） Genome-based drug design cDNA chip cDNA MicroArrays DNA MicroArrays use hybridization technology to examine gene expression Attach different DNAs onto a slide as a grid of small spots, one for each gene - up to 50,000 per slide Hybridize a mixture of fluorescently labeled cDNAs extracted from cells after different treatments - control is green and experimental is red Examine expression patterns by looking at levels of fluorescence for all genes in array Extract mRNA Convert to cDNA and Label with Fluorescent Dyes Mix Labeled cDNA Hybridize cDNA to the Slide Excite Dyes with Laser Scan Quantify Signals Affymetrix GeneChip technology (Summary) Short (25 mer) Oligonucleotides 40-60k DNA oligos on ~ 2.5 cm2 glass surface. Technology combines oligonucleotide synthesis with photolithographic computer chip technology. The oligonucleotides are synthesized on the slide. A probe set = 11-20 PM, MM pairs Spotted vs. Affymetrix arrays Spotted cDNA arrays| Affymetrix arrays Background Datasets Results Background For cDNA micrarrays, multiple clones are also measured for a transcript to evaluate the consistency of microarray data. Ideally, such multiple clones, especially the replicate ones, should have similar measurements. The multiple clones can be classified into two types: different sequence segments for a transcript (DC ) replicate sequence segment for a transcript (RC) 对应基