1. FastMap Tutorial

2. Installation Requirements Computer with 2GB of RAM JAVA Runtime Environment (JRE) 6 http://java.sun.com/javase/downloads/?intcmp =1281

3. How to launch FastMap Unzip the FastMap.zip file anywhere Executable files in the directory: FastMap.exe FastMap.bat FastMap.alt.bat

4. How to launch FastMap To launch the application: Double-click on FastMap.exe If FastMap.exe doesn’t work: Double-click on FastMap.bat

5. How to launch FastMap If the application cannot be launch with FastMap.exe or FastMap.bat: Edit FastMap.alt.bat Put the path of the directory where the JAVA 6 JRE is installed in the variable JAVA_HOME

6. How to launch FastMap Put the path of the directory where the JAVA 6 JRE is installed in the variable JAVA_HOME

7. Interface

8. Menus Tasks buttons Genes List Progress bar Cancel task buttons Chart

9. Association Plot Correlation Values SNPs Threshold levels 99% 95% 50% ChromosomeGene 90%

10. Menu File menu (short cut: Alt+F) Open and load a gene expression file (short cut : Alt+F then G or Ctrl+G) Tasks buttons Open and load a SNP file (short cut : Alt+F then N or Ctrl+N) Open and load a HapMap SNP File (short cut : Alt+F then H or Ctrl+H) Open and load Transposed PLINK file (short cut : Alt+F then R or Ctrl+R) Quit the application (short cut : Alt+F then Q or Ctrl+Q)

11. Association menu (short cut: Alt+A) Menu Plot the Correlation or F-Statistic (short cut : Alt+A then P or Ctrl+P) Write the Correlation or F-Statistic into files (short cut : Alt+F then W or Ctrl+W) Save the plotted chart (short cut : Alt+F then C or Ctrl+C) Open the UCSC browser (short cut : Alt+F then U or Ctrl+U) Write LocusZoom ready chromosome data file (short cut : Alt+F then L or Ctrl+L)

12. Menu Tools menu (short cut: Alt+T) Open the option window (short cut : Alt+A then O or Ctrl+O) Open the SNP Similarity window Open the SNP Analysis window

13. Options window

14. SNP similarity window Allow two groups to be defined based on SNP similarity and to perform a mean or median subtraction on each group values for the correlation or F-statistic. The checked strains form the first group and the unchecked strains form the second group.

15. SNP similarity window Example of two groups

16. SNP similarity window Example of two groups

17. Input files The application expects either: A gene expression file and SNP file that are both tab delimited text files. Or a gene expression file and a tree file which is a binary file produce by FastMap.

18. Input files All the strains that are in the gene expression file must be in the SNP file. The strain order does not matter. The SNP file can contain more strains than the gene expression file.

19. Gene expression file Fist line is the header Microarray probe ID Something more meaningful like the gene name Strains Gene expression data FastMap will display this

20. SNP data file Strains Chromosome Mb position SNP

21. Select the association type Set the association type Correlation: window size = 1 F-Statistic: window size > 1 Recommended size = 3

22. Load the files Open and load a gene expression file (short cut : Alt+F then G or Ctrl+G) Tasks buttons Open and load a SNP file (short cut : Alt+F then N or Ctrl+N) The files can be loaded by using the menu or the buttons bar

23. Plot a chart Right-click on a gene name Double-click on a gene name

24. Association chart Zoom in or out by using the mouse wheel or by selecting an area

25. UCSC browser Send data to UCSC browser if the current view is on a single chromosome.

26. UCSC browser FastMap track

27. LocusZoom ready files FastMap allows the user to write LocusZoom ready files to send results directly to LocusZoom, which will plot genes and SNP annotation in a specified region of interest.

28. LocusZoom ready files Write LocusZoom ready files.

29. Write associations Set the default output directory where the correlation or F-statistic files will be written Set what output files will be written Set writing options

30. Write association Right-click on a gene name Several genes can be selected