3 Concept of Genevestigator Tissue type 1Tissue type 2Tissue type 3Tissue type 4…Tissue type 200…Thousands of microarrayexperiments world-wideCuration of data and annotationModel of a summarizedoutputCuration: normalization and annotation of- Anatomy- Development- Stimulus and MutationEstablishment of theGenevestigatorDatabase
4 Curation: quality control of microarray data Unprocessed probe intensityRNA degradation plotsProbe-level analysis (RLE, NUSE)Border element analysisArray-array correlation plots
5 Overview of the Genevestigator System Database and Application Server ClusterWebsiteJava Client Application
7 Genevestigator CLASSIC tool: Meta Profile Analysis
8 Meta Profile Analysis: analytical approach genesAnatomy[space]Development[time]Stimulus /Mutation[response]which conditions?
9 Meta-Profile Analysis 1. Chose an organism2. Enter the genes you wish to work with
10 Meta-Profile Analysis View and interpret the results across:Anatomical categories (Anatomy tab)Developmental stages (Development tab)Chemicals, diseases, treatments, etc. (Stimulus tab)Genetic modifications (Mutation tab)Tumor types (Neoplasm tab)
11 Meta-Profile Analysis: Anatomy tool Looks at how genes are expressed in different tissuesMean and standard deviationAnatomy categories as a tree (ontology); expand / collapseNumber of arrays per category is indicatedLooks at how genes are expressed in different tissuesMean and standard deviationAnatomy categories as a tree (ontology); expland / collapseNumber of arrays per category is indicatedAnatomical expression profile of ß-Actin in the mouse
12 Meta-Profile Analysis: Development tool Looks at how genes are expressed during the life cycle of an organismExample for humanExample for mouse / ratExpression profile of BDNF across thehuman development
13 Meta-Profile Analysis: Stimulus and Mutation tools Most upregulating conditionsList (or tree)of variousconditionsSpots indicate theresponses of selectedgene(s) to the list of conditionsMost downregulating conditions
14 Meta-Profile Analysis: Neoplasm tool Looks at how genes are expressed in different tumorsMean and standard errorTumors ordered as a tree (ontology); expand / collapseNumber of arrays per category is indicatedLooks at how genes are expressed in different tissuesMean and standard deviationAnatomy categories as a tree (ontology); expand / collapseNumber of arrays per category is indicatedExpression profile of NPY1 receptor across human tumors
26 Useful features - tooltips Tooltips (mouse-over) provide detailed information abouta treatment, a spot, or an experiment.
27 Focus function Focus on an array selection Focus on a gene selection tools will compile results from this combination of dataallows to easily jump from one selection of genes or arrays to another selectionNote: be sure that genes and organism/arrays are compatible!(e.g. you cannot look at mouse genes in a selection of rat arrays…)27
29 Exporting data Export content: Mean value Standard error values Export format:tab-delimited (TXT) orcomma-separated (CSV)
30 Saving workspaces Saves content of selections: selections of experiments and arraysselections of genesstatus of checkboxesBenefits:allows to share results between colleaguesallows to continue your research at a later stage without losing the context