转录组注释.pptVIP

大规模芯片meta-analysis的流程-GEOgle 通过对基因表达数据库Gene Expression Omnibus（GEO）、Medical Subject Headings (MeSH)和信号转导数据库sigPathway数据进行整合，开发了文本挖掘工具GEOGLE。用户可以同过词条、GDS ID、gene IDs及通路名等多种查询方式，对其相关的实验数据、通路和生物的方面进行查询。此外，GEOGLE通过GDSes的子集总结了信号基因，对基因表达和表型差异进行了相关性的评价。GEOGLE通过荟萃分析（Meta-analysis）方法对不同实验中获得的基因表达和表型差异进行定量地分析。 (:14000/kweb/workflow.jsp?id=00020)。相关文章已发表（BMC Bioinformatics 2009, 10:264） A: The title for the miner B: A button for closing this miner after using C: Some special optional parameters for instance set FALSE for listMeshGDS.only as default will make the miner search all related information including Gene and Pathway according to the query, which is believed taking a longer time. A fast search for only MESH words and GDS IDs could be done with TRUE set for the parameter, no results will be returned by clicking Gene or Pathway button. D: The output buttons. Please use any of them to get the results * Gene expression profiling has been widely used in biological research. The advantage of this technology is, it can monitor the expression of thousands of genes simultaneously. * We aim to develop a large scale meta-analysis approach to understand this genomic characteristic of human genes. * The main idea is, calculate the position of standard deviation of each gene in each data set, and for hundreds of data sets, test if gene’s positions are enriched at the top or bottom of that of the whole gene list. We calculate a Sensitivity Score (SS) for each gene. * rank was calculated by average the standard deviation rank of a gene across all the datasets. The robust genes tend to have simpler regulatory mode, which makes the system more stable. * Degree is defined as the number of direct neighbors of a node v in the network G. Betweenness centrality is calculated as the fraction of number of shortest paths that pass through each node, and then normalized by b=b/(n-1)(n-2) where n is the order of network. Closeness centrality is calculated as (1/average distance to al