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April 2004

Microarray Data Management. Jianwei (Jerry) Li. April 2004. Scanner. Image Analysis. .tiff Image File. Raw Gene Expression Data. Gene Annotation. Normalization / Filtering. Normalized Data with Gene Annotation. Expression Analysis. Data Entry / Management.

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April 2004

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  1. Microarray Data Management Jianwei (Jerry) Li April 2004 test

  2. Scanner Image Analysis .tiff Image File Raw Gene Expression Data Gene Annotation Normalization / Filtering Normalized Data with Gene Annotation Expression Analysis Data Entry / Management Interpretation of Analysis Results MAD Others… Database AGED Database Database Microarray Data Flow Printer test

  3. Microarray Database Microarray Experiment and Annotation Control Test Prepare Fluorescently Labeled Probes Obtain RNA Samples Hybridize, Wash Scanning MADAM test

  4. Requirements of MADAM • Communicates with a DBMS. • Uploads microarray information to database with a convenient way. • Allows users to view the information. • Retrieves the information and converts it to a data format for analysis. • Checks errors for the data entries. • Starts other tools to manipulate the data. test

  5. Microarray Database Functions of MADAM Data Display Data Entry Other Tools Data Retrieve MADAM Protista test

  6. Slide Slide_name id slide_type config_id slide_lot bar_code run_id storage_id Microarray Database Microarray Database Schema test

  7. Clone New_plate Expt_probe Experiment Study Expression Slide Probe Slide_type Spot Probe_source Hyb Protocol Primer_pair Primer Gene PCR Scan Analysis Normalize Conceptual Schema: MAD test

  8. Interface of MADAM Tool Bar Navigation Panel Working Panel Log Panel test

  9. Data Entry … test

  10. Procedures of Data Entry 1. Enter an organism name using New Organism Window. 2. Upload your plate and PCR information with PCR Score. 3. Insert study information with Study page. 4. Insert probe data with Probe and Probe Source pages. 5. Use other pages ... test

  11. PCR File Format - 1 Type 1: 7-Column Gene or Clone Feat Name / Locus Primer 1 Sequence Primer 2 sequence Amplified Value Primer 1 Name Primer 2 Name Length test

  12. PCR File Format - 2 Type 2: 8-Column Gene or Clone Feat Name Primer 1 Sequence Primer 2 sequence Amplified Value Primer 1 Name Primer 2 Name Length Locus test

  13. PCR File Format - 3 Type 3: Oligo 5' end Feat Name Primer Name Amplified Value 3' end Tm Locus Sequence test

  14. Procedures of Data Entry 1. Enter an organism name using New Organism Window. 2. Upload your plate and PCR information with PCR Score. 3. Insert study information with Study page. 4. Insert probe data with Probe and Probe Source pages. 5. Use other pages ... test

  15. Data Entry With Study Page a chemical or factor that is used for treatment in a study (H2O, light, NaCl). Time : 10 : Hour Time : 5 : Day Temperature : 30 : ºC 10% NaCl : 100 : ml test

  16. Introduction of Slide Type • Not the type of slide manufacturers produced. • Array type that describe how the array was constructed. test

  17. Interface of Slide Type test

  18. config id machine slide_type pins_x pins_y dist_x dist_y … Format of Slide Name c a g 0 0 5 a 0 0 3 6 Project Name Glass Type Consequential Number Config_id test

  19. Functions of Other Pages inserts the locations of the image files and scan parameters into database. Scan uploads the intensities (mev or tav files) of an experiment to database. Expression saves normalized intensities to database (unavailable). Analysis test

  20. Data Report … test

  21. Data Retrieve … test

  22. Data Retrieve with Miner select experiment. check what amplified value to be zero. select output file format. provide file name. start to retrieve. test

  23. mev and tav File Format Intensities Spot positions Backgrounds Flags test

  24. MGED, MIAME, and MAGE-ML • Microarray Gene Expression Data Society Goal: facilitate microarray data exchange between scientists • Working Groups: *Experiment description standards (MIAME) *Data exchange format (MAGE-ML) *Ontologies for sample description • Minimal Information About Microarray Experiments. *Minimal description of a set of microarray experiments. • MicroArray Gene Expression Markup Language. *XML based means of exchanging microarray data test

  25. ArrayExpress: Public Repository test

  26. MIAMExpress: Data Submission Tool test

  27. MAGE-ML Nodes slide: how a slide is generated slide type process of making slide probe sequence spots on slide researchers who conduct the experiments probe source study hybridization expression intensity how to measure intensities test

  28. MAGE-ML Export with Madam provide person’s info. indicate the role (submitter, researcher, …) of the person. select an experiment to be written out. provide a file name. start the writing. test

  29. MAGE-ML Output of Experiment test

  30. Other tools … test

  31. Query Window type SQL code. click the Submit button. view the query results. save the query results. test

  32. indicate the compare relationship with arrows or chart. Experiment Designer set the number of samples (probes). save the picture. test

  33. Express Converter for GenePix, Image, ScanArray, TAV, and MEV files. set a number of files to be converted. output files have the same names & paths with diff. extension. change the file names or paths if you want. start converting. test

  34. Microarray Database Functions of MADAM Data Display Data Entry Other Tools Data Retrieve MADAM Protista test

  35. Acknowledgements TIGR Microarray Software Team John Quackenbush Nirmal Bhagabati John Braisted Tracey Currier Eleanor Howe Jerry Li Wei Liang Alexander I. Saeed Vasily Sharov Mathangi Thaiagarjian Joseph White test

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