test 1

April 2004

Microarray Data Management

Jianwei (Jerry) Li

test 2

Microarray Data FlowPrinter

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

test 3

MADAMMADAM

Microarray Experiment and Annotation

Prepare FluorescentlyLabeled Probes

Control

Test

Hybridize, WashObtain RNA Samples

Scanning

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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

Functions of MADAM

Data Entry

ProtistaProtistaMADAMMADAM

Other Tools

Data Display

Data Retrieve

test 6

Microarray Database Schema

SlideSlide

Slide_nameididslide_typeslide_typeconfig_idconfig_idslide_lotslide_lotbar_codebar_coderun_idrun_idstorage_idstorage_id

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Conceptual Schema: MAD

ProtocolPrimer_pair

Primer

PCR

Slide

Scan Analysis Normalize

Experiment Study

Hyb

Expt_probe

Expression

Probe_source Probe

Gene

Slide_type Spot

Clone

New_plate

test 8

Interface of MADAM

Tool Bar

Navigation Panel

Working Panel

Log Panel

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Data Entry …

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Procedures of Data Entry

1. Enter an organism name using

New Organism Window.

5. Use other pages ...

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.

test 11

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

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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

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PCR File Format - 3

Amplified Value

Type 3: Oligo

Feat Name Primer Name

Sequence 3' end Tm

5' end

Locus

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Procedures of Data Entry

1. Enter an organism name using

New Organism Window.

5. Use other pages ...

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.

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 : DayTemperature : 30 : ºC10% NaCl : 100 : ml

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

Printer / Arrayer:Number of pens,

Print pattern.

Slide:Number of spots,

Space between spots

Plates:how they were

ordered on printer.

Slide Type

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Interface of Slide Type

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Format of Slide Name

c a g 0 0 5 a 0 0 3 6c a g 0 0 5 a 0 0 3 6

Project Name

Config_id

Glass Type

Consequential Number

configconfig

idmachinemachineslide_typeslide_typepins_xpins_xpins_ypins_ydist_xdist_xdist_ydist_y……

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Functions of Other Pagesinserts the locations of the image files and scan parameters into database.

ScanScan

ExpressionExpression

AnalysisAnalysis

uploads the intensities (mev or tav files) of an experiment to database.

saves normalized intensities to database (unavailable).

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Data Report …

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Data Retrieve …

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Data Retrieve with Miner

select experiment.

check what amplified value to be zero.

select output file format.

provide file name.

start to retrieve.

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mev and tav File Format

Spot positions Intensities Backgrounds Flags

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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

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ArrayExpress: Public Repository

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MIAMExpress: Data Submission Tool

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MAGE-ML Nodes

slide: how a slide is generated

slide typeprocess of making slide

probe sequence

spots on slide

researchers who conduct the experiments

probe source

study hybridization

expression intensity

how to measure intensities

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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.

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MAGE-ML Output of Experiment

test 30

Other tools …

test 31

Query Window

type SQL code.

click the Submitbutton.

view the query results.

save the query results.

test 32

Experiment Designer

set the number of samples (probes).

indicate the compare relationship with arrows or chart.

save the picture.

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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.

test 34

Functions of MADAM

Data Entry

ProtistaProtistaMADAMMADAM

Other Tools

Data Display

Data Retrieve

test 35

AcknowledgementsTIGR Microarray Software Team

John Quackenbush

Nirmal BhagabatiJohn BraistedTracey CurrierEleanor Howe

Jerry LiWei Liang

Alexander I. SaeedVasily Sharov

Mathangi ThaiagarjianJoseph White