WORKING WITH ARABIDOPSIS AFFYMETRIX DATA Day1 Data Sources, Normalisation and NASC Affy Web Site Tools Practical • • • OPTIONS The Practical session is flexible so that you can concentrate on whatever interests you. – – – 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. – 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 – – – – – 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 • GeneSpring is installed on Martin’s laptop, which will be available for use throughout the practical session. • D-Chip will be available on CD to be installed onto computers on request. • The day’s speakers will also be available to discuss their subjects. – 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 – – – – 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 – – – – 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 • http://affymetrix.arabidopsis.info/narrays/twogenescatter.pl • Enter “AT1G14920” (GAI) and “AT2G01570” (RGA) and plot • Select spots from the ATH1 chip – • rather than those from the older AG chip The relationship between the 2 genes is now visualised. – What does it suggest • Repeat for a gene you are interested in! • Think about: – – – 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.