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Bioinformatics for “Gene Expression Analysis in Diagnostic Medicine”

Bioinformatics for “Gene Expression Analysis in Diagnostic Medicine”. Follow-up Course, 20 to 25 November 2006 CAS-MPG Partner Institute for Computation Biology, Shanghai. 1. Goals of this Course 2. Course Outline 3. TIGR Software Suite TM4 4. Using Apple computers. Goals.

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Bioinformatics for “Gene Expression Analysis in Diagnostic Medicine”

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  1. Bioinformatics for“Gene Expression Analysisin Diagnostic Medicine” Follow-up Course, 20 to 25 November 2006 CAS-MPG Partner Institute for Computation Biology, Shanghai

  2. 1. Goals of this Course2. Course Outline 3. TIGR Software Suite TM44. Using Apple computers

  3. Goals • Obtain raw expression values from scanned slides • Perform quality checks • Produce comparable expression values through normalization • Explore data with clustering methods • Find significantly expressed genes

  4. 1. Goals of this Course2. Course Outline 3. TIGR Software Suite TM44. Using Apple computers

  5. Outline | Monday Tuesday Wednesday Thursday Friday --------------------+------------------------------------------------------------------------------------------------ 8:30 Computer- | Seminar room: Practise with Practise with Practise with Practise with room | - Welcome Manila data: Manila data: MeV on: drosophila data: | - Introduction - Get raw values - Get expression - Differential - Clustering 10:30 (Coffee) | Computer room: (Spotfinder) data (MIDAS) expression (Mev) | - using Macs - Clustering (MeV) - Multiple - Compare to | - starting testing Angela's work | Spotfinder --------------------+------------------------------------------------------------------------------------------------ 13:30 Lunch | --------------------+------------------------------------------------------------------------------------------------ 14:30 Seminar- | Lectures: Lectures: Lectures Lectures Final: room | - Image processing - Normalisation (Christ.+Dennis): (Angela): - Demo of | (Spotfinder) (MIDAS software) - Differential - Identification databases 16:00 (Coffee) | - Quality checks - Clustering Expresssion of glial gene - General | - Workflow and methods - Multiple in drosophila discussion | data file types (MeV software) Testing - Discussion of | experiment design --------------------|------------------------------------------------------------------------------------------------ 17:30 End |

  6. 1. Goals of this Course2. Course Outline 3. TIGR Software Suite TM44. Using Apple computers

  7. Printer Scanner TIGR Software Suite TM5 .tiff Image File Image Analysis Raw Gene Expression Data Gene Annotation Normalization / Filtering Normalized Data with Gene Annotation Expression Analysis Interpretation of Analysis Results

  8. Goals of this Course2. Course Outline 3. TIGR Software Suite TM44. Using Apple computers (and viewing MA slides)

  9. Using Apple computers

  10. Using Apple computers The Menu bar of the current application Two Finder windows (like Windows Explorer) The Finder Sidebar provides links to important folders The Dock holds running and most used applications

  11. Using Apple computers The Apple menu holds general items, such as: Logout Here is all our course data: /picb/course/ Preferences Safari Webbrowser Activity Monitor Finder

  12. Using Apple computers Practising steps: • Obtain login account and password from lecturer • Login and familiarize with Finder • Locate /Applications/System Preferences.app and use it to enable right mouse button • Remove unneeded items from Finder Sidebar and from Dock • Locate /Applications/Utilities/Activity Monitor.app and activate Memory Usage and CPU Monitor • Locate /picb/course/Applications and add it to Finder Sidebar • Start TIGR-Spotfinder311.app (through Sidebar) • In Spotfinder, view some Microarray slides from Manila, located in /picb/course/10-Manila-Slides/

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