test1 April 2004 Microarray Data Management Jianwei (Jerry) Li

test2 Microarray Data Flow Printer Image Analysis Database AGED Database Others… Database MAD Raw Gene Expression Data Normalized Data with Gene Annotation Interpretation of Analysis Results.tiff Image File Gene Annotation Scanner Normalization / Filtering Expression Analysis Data Entry / Management

test3 MADAM Microarray Experiment and Annotation Prepare Fluorescently Labeled Probes Control Test Hybridize, Wash Obtain RNA Samples Scanning

test4 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.

test5 Functions of MADAM Data Entry Protista MADAM Other Tools Data Display Data Retrieve

test6 Microarray Database Schema Slide Slide_name id slide_type config_id slide_lot bar_code run_id storage_id

test7 Conceptual Schema: MAD Protocol Primer_pair Primer PCR Slide Scan Analysis Normalize Experiment Study Hyb Expt_prob e Expression Probe_source Probe Gene Slide_type Spot Clone New_plate

test8 Interface of MADAM Tool Bar Navigation Panel Working Panel Log Panel

test9 Data Entry …

test10 Procedures of Data Entry 1. Enter an organism name using New Organism Window. 5. Use other pages 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.

test11 PCR File Format - 1 Amplified Value Type 1: 7-Column Gene or Clone Feat Name / Locus Primer 1 Name Primer 1 Sequence LengthPrimer 2 Name Primer 2 sequence

test12 PCR File Format - 2 Amplified Value Type 2: 8-Column Gene or Clone Feat Name Primer 1 Name Primer 1 Sequence LengthPrimer 2 Name Primer 2 sequence Locus

test13 PCR File Format - 3 Amplified Value Type 3: Oligo Feat NamePrimer Name Sequence 3' end Tm 5' end Locus

test14 Procedures of Data Entry 1. Enter an organism name using New Organism Window. 5. Use other pages 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.

test15 Data Entry With Study Page a chemical or factor that is used for treatment in a study (H 2 O, light, NaCl). Time : 10 : Hour Time : 5 : Day Temperature : 30 : ºC 10% NaCl : 100 : ml

test16 Introduction of Slide Type  Not the type of slide manufacturers produced.  Array type that describe how the array was constructed. Slide Type Plates: how they were ordered on printer. Slide: Number of spots, Space between spots Printer / Arrayer: Number of pens, Print pattern.

test17 Interface of Slide Type

test18 Format of Slide Name c a g a Project Name Config_id Glass Type Consequential Number config id machine slide_type pins_x pins_y dist_x dist_y …

test19 Functions of Other Pages inserts the locations of the image files and scan parameters into database. Scan Expression Analysis uploads the intensities (mev or tav files) of an experiment to database. saves normalized intensities to database (unavailable).

test20 Data Report …

test21 Data Retrieve …

test22 Data Retrieve with Miner select experiment. check what amplified value to be zero. select output file format. provide file name. start to retrieve.

test23 mev and tav File Format Spot positions I n tensities Backgrounds Flags

test24 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

test25 ArrayExpress: Public Repository

test26 MIAMExpress: Data Submission Tool

test27 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

test28 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.

test29 MAGE-ML Output of Experiment

test30 Other tools …

test31 Query Window type SQL code. click the Submit button. view the query results. save the query results.

test32 Experiment Designer set the number of samples (probes). indicate the compare relationship with arrows or chart. save the picture.

test33 Express Converter for GenePix, Image, ScanArray, TAV, and MEV files. set a number of files to be converted. change the file names or paths if you want. start converting. output files have the same names & paths with diff. extension.

test34 Functions of MADAM Data Entry Protista MADAM Other Tools Data Display Data Retrieve

test35 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