Upload
moris-summers
View
220
Download
0
Tags:
Embed Size (px)
Citation preview
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
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
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
test 7
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
test 9
Data Entry …
test 10
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
test 12
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
test 13
PCR File Format - 3
Amplified Value
Type 3: Oligo
Feat Name Primer Name
Sequence 3' end Tm
5' end
Locus
test 14
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
test 16
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
test 17
Interface of Slide Type
test 18
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……
test 19
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).
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
Spot positions Intensities 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 typeprocess 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 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.
test 33
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