GEOGeneExpressionOmnibusGEO基因表达数据库.pptVIP

GEO Gene Profiles GEO Gene Profiles Querying GEO with IDs from Papers A common way to access GEO data is through accessions from papers. Online journals include hyperlinks to the GEO accession page. Or, at the GEO home page enter the accession into the QueryGEO accession text box GEO Links in PubMed Search Results One option for displaying PubMed search results is GEO DataSet links. When present, the results page is actually from Entrez GEO DataSets. GEO BLAST * * * * * * * * * * * * * * * * Gene Expression Omnibus (GEO) /geo/ Microarrays in gene expression A typical gene expression analysis experiment: Differential systems – e.g. cancer vs. normal, drug vs. no drug Choose/prepare the microarray Extract total mRNA (transcriptome) Reverse transcription/dye labeling Combine equal amounts Hybridize Scan ANALYSE AND INTERPRET THE RESULTS – this is the tricky part… Microarrays in gene expression SPOTS Hybridization SCAN A public repository for the archiving and distribution of gene expression data submitted by the scientific community. Curated, online resource for gene expression data browsing, query, analysis and retrieval.  Convenient for deposition of gene expression data, as required by funding agencies and journals. Gene Expression Omnibus (GEO): Gene Expression and Molecular Abundance Data Repository GEO Architecture Platform (GPL) = the technology used and the features detected. Sample (GSM) = preparation and description of the sample. Series (GSE) defines a set of samples and how they are related. DataSets (GDS) sample data collections assembled by GEO staff. GEO has four kinds of data records GPL Platform descriptions GSM Raw/processed spot intensities from a single slide/chip GSE Grouping of slide/chip data “a single experiment” GDS Grouping of experiments Curated by NCBI Submitted by Experimentalists Submitted by Manufacturer GEO Architecture GEO Home Page Simple interface to: show status find documentation query data browse data Pl