微阵列数据分析工具.ppt

1、微阵列数据分析工具,2007-5-31 闫微,2,3,Experiment vs Contro Log Ratiol,4,Gene identifiers,5,表达下调2倍以上的基因有3810个、8倍以上的基因有197 如何对这些差异表达的的基因的生物学意义进行解释？,6,需要有一组微阵列实验数据的解释工具 GOstat Panther MILANO Genomatix,7,Prepare input data,Gene identifiers 1. Gene symbols (e.g. icam3) 2. Gene description (e.g. mitogen-activated pr

2、otein kinase 1) 3. Entrez gene identifier or GeneID (e.g. LOC5166 or 5166) 4. RefSeq ID (e.g. NM_02044) 5. ,8,GOstat,.au/ GO数据库是注释和分析基因功能的有效工具.微阵列实验往往会产生大量的基因列表.为了获得这类型数据的生物学意义,我们需要找到这些数据的功能注释或是能代表它们的GO分组. GOstat程序就是用来分析这个的基因列表, 根据GO注释的功能进行分类.,9,10,11,12,13,Benefits of Ontology

3、Stats,Often find insight into changes in cellular function which were not obvious from the gene list. Genes in the same ontology group are often in the same pathway or co regulated.,14,Panther,/ PANTHER (Protein ANalysis THrough Evolutionary Relationships)分类系统按照基因功能来分类的唯一资源,用公

4、布的科学实验证据和进化关系来预测功能.随着蛋白质数据量的增加,生物学家得到了规范化的通路中的详细的生物相互作用,而且可用交互式的方法显示出来. 通过其Gene expression tools可用大规模的搜索现有基因的信号通路(Pathway )、分子功能（Molecular Function)及生物学进程(Biological Process )。PANTHER英文意义是豹，该网站的目的即是生物工作者在大规模的信息中，像猎豹一样搜寻到有意义的信息。,15,Gene expression tool,16,17,18,19,MILANO -Microarray Literature-based

5、Annotation,http:/milano.md.huji.ac.il/ Milano , a cool program developed by Ran Rubinstein at The Hebrew University of Jerusalem is released. This program performs automatic searches in PubMed or the GeneRIF collection for articles containing co-occurrences of search terms with a list of genes (e.g.

6、 from a microarray experiment).The program is used by pasting the list of Gene IDs or symbols in the Primary Search Term field, and the list of cross-reference search terms in the Secondary Search Term field. The output is a table containing the number of hits for each pair of search terms.,20,paste

7、 the list of Gene IDs or symbols,paste the list of cross-reference search terms,21,22,23,24,Genomatix,http:/www.genomatix.de/ 用来研究基因调控的分子机制 Genomatix网站下属的软件BiblioSphere软件可以将已知的基因进行汇总分析，根据已有的信号通路和文献，得出所有输入基因的相互联系图，对基因中重要基因的筛选有较重要的意义。同时，它也可以将这些基因按照疾病的不同进等分类，有比较好的治疗指导的意义。,25,price,26,软件界面,27,登录之后的界面,28

8、,1.Create a new Project 2.Create a new Analysis,Gene identifiers can be entered as a list separated by white spaces, commas or semicolons.,29,View networks,30,Input genes + transcription factor,31,Metabolic pathways,Signal transduction,32,33,Final Outcome,By using a combination of the tools available we hope to come u