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WORKING WITH ARABIDOPSIS AFFYMETRIX DATA
Day1
Data Sources, Normalisation and NASC Affy Web Site Tools
Practical
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OPTIONS
The Practical session is flexible so that you can concentrate on whatever interests you.
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You have choice of working through this practical
or software tutorials
or just trying things out and asking questions.
This PowerPoint file contains a short optional practical on data download and NASC
tools.
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a guided tour of these tools is also available at:
http://affymetrix.arabidopsis.info/narrays/static/NASCArraysTutorial.pdf
J-Express is installed on all the computers in the room
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The combination code for the room can be got from the school office
most recent version at start> All Programs> J-Express pro 2.5
The shortcut on most desktops links to an older version
Zoë's talk can take you through several stages of its use
Paddy’s J-Express tutorial for spotted arrays can be found at:
http://plantsci.arabidopsis.info/pg/jxtutorial.doc
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GeneSpring is installed on Martin’s laptop, which will be available for use throughout the
practical session.
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D-Chip will be available on CD to be installed onto computers on request.
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The day’s speakers will also be available to discuss their subjects.
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others attending the workshop will have expertise to share too.
Download Data From NASC
• Download data for selected Chips
– over all genes
• http://affymetrix.arabidopsis.info/narrays/experimentbrowse.pl
• Try searching by keyword
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E.g. Search for Auxin
Chose an experiment and click.
You could download whole experiment
Instead chose one chip and add it to your selection
• Try searching by slide search
– E.g. Search for ethylene treated petioles
– chose one chip and add it to your selection
• Try searching by tree view
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E.g. Look for a root developmental series
E.g. Look for experiments done by Cathlene Eland
You could download whole experiment
Instead chose one chip and add it to your selection
Selection
• Click Selection at the top of the page
– You could download your selection
– look at the options in the dropdown menu
Bulk Gene Download
• Download data for selected Genes
– over all chips
• http://affymetrix.arabidopsis.info/narrays/help/psp-wbubn.html
Spot Histories
• http://affymetrix.arabidopsis.info/narrays/spothistory.pl
• Enter “At4g18960” (agamous) and plot
• Select a spot from the ATH1 chip
– rather than those from the older AG chip
• Click on the bar with the highest signal shown
– All samples in this signal bracket are now listed below
• Click on “Bio Source 1 Data” for any of those samples
– Biological information on sample is now given (for all samples)
– What do they have in common
– What does this suggest about the gene
• Repeat for “At5g09810” (actin)
– What does the position of the peek suggest about the gene
• Repeat for a gene you are interested in!
Gene Swinger
• http://affymetrix.arabidopsis.info/narrays/geneswinger.pl
• Enter “At4g18960” (agamous) and swing
• Select a spot from the ATH1 chip
– rather than those from the older AG chip
• Experiments in which the gene most varies are now given
– What do they have in common
– What does this suggest about the gene
– View an experiment that interests you
• Repeat for a gene you are interested in!
Two Gene Scatterplot
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http://affymetrix.arabidopsis.info/narrays/twogenescatter.pl
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Enter “AT1G14920” (GAI) and “AT2G01570” (RGA) and plot
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Select spots from the ATH1 chip
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rather than those from the older AG chip
The relationship between the 2 genes is now visualised.
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What does it suggest
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Repeat for a gene you are interested in!
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Think about:
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If there are more points in one bracket then another along an axis then you must expect to
see more outliers in that bracket. They do not necessarily signify a correlation.
Using log scales may lessen this illusion.
From the chip selection page (see slide 3), you can do a two gene scatterplot over your
chosen chips only. This may help differentiate between (e.g.) a repression relationship within
a tissue and two genes which are expressed in different tissues.
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