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Unformatted text preview: 1 von 15 MapMan Help 1 Short Introduction 1.1 View data included in the package 1.2 Display options 1.3 Print 1.4 Save 1.5 Search Functions 1.6 Statistics (Wilcoxon Rank Sum Test) 2 View your own Arabidopsis 22KAffymetrix data 2.1 Data format 2.2 Create an experiment folder 2.3 Add data files to your new folder 2.4 Visualise your data 3 Use MapMan to visualise any gene expression, metabolite or other data 3.1 Creation of a mapping file 3.2 Create your own pathway (Annotation of an image file) 3.3 Histogram frequency chart 4 Structure of MapMan 5 Available Pathways Overview 6 Contact information 1 Short introduction index MapMan is a user-driven tool that displays large datasets, e.g. from gene expression experiments onto diagrams of metabolic pathways or other processes. You can not only use the provided diagrams, but also generate your own ones and let the software display yours and others data onto your diagrams. There are three different types of files needed to use MapMan. They are located in three different folders inside the directory of example data. (i) data files: contain experimental results ( .xls or .txt file format) (ii) pathways: diagrams ( .bmp file format) which serve as context (iii) mapping files: connects gene/metabolite/protein identifiers to BINs (functional categories) which are displayed (. xls or . txt file format) 2 von 15 1.1 View data included in the package index The MapMan download provides example. After starting the MapMan software you will find data files in the Experiments folder, pathway image files in the Pathways ( overview of available predefined pathways )folder and mapping files in the Mappings folder of the selection directory on the left. You can view the included datasets in context of different metabolic pathways (i) Double click an image file from the folder " Pathways ", e.g. "Metabolism_overview" or "Glycolysis". Choose a mapping file from the pop-up box and click "OK". Choose "AFFY2005" in combination with "Metabolism_overview" with all maps showing biological processes (This is most often right). Hint : Images need different mapping files (table 1) . Response_images need an Response_mapping file. (In fact, if you dont care about the statistics you can combine both files). (ii) A simple click activates experiment files from the folder " Experiment : DiurnalCycle (or other) one by one. All data files from one experiment can now be viewed in sequence. Each file is called up after loaded the first time by mouse click in a fraction of a second. Each gene is symbolised by a box, the gene expression level is colour-encoded ( red = down-, blue = upregulation). A simple mouse-over action on an individual box will call up the gene annotation beneath your mouse, while a click will copy the information to the text window below pathway....
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This note was uploaded on 08/01/2009 for the course HORT hor-11-12 taught by Professor Park during the Spring '09 term at A.T. Still University.
- Spring '09