Research Simulation
The Spotted Microarray workflow - GenePix and the Ramhorn Array Database
(August 4)

Time: Wed-Thu, August 4, 9:00 am - noon
Place: Bioinformatics Computer Core Lab (Rm 104), Life Sciences Bldg
Organizer: Paul Fawcett
Audience: Primarily 1st year students

Topics of the session

Spotted Microarrays
Axon GenePix - microarray image analysis
Archiving Microarray data with the Ramhorn Array Database
Microarray analysis with the Ramhorn Array Database
Significance Analysis of Microarrays (SAM)
Cluster and Treeview

Resources for the session

Suggested Reading (for both days): Note that links are directly to .PDF files.

Lieb JD, Liu X, Botstein D, Brown PO. Promoter-specific binding of Rap1 revealed by genome-wide maps of protein-DNA association. Nat Genet. 2001 Aug;28(4):327-34

Diehn M, Eisen MB, Botstein D, Brown PO. Large-scale identification of secreted and membrane-associated gene products using DNA microarrays. Nat Genet. 2000 May;25(1):58-62

Pollack JR, Sorlie T, Perou CM, Rees CA, Jeffrey SS, Lonning PE, Tibshirani R, Botstein D, Borresen-Dale AL, Brown PO. Microarray analysis reveals a major direct role of DNA copy number alteration in the transcriptional program of human breast tumors. Proc Natl Acad Sci U S A. 2002 Oct 1;99(20):12963-8

Wang D, Urisman A, Liu YT, Springer M, Ksiazek TG, Erdman DD, Mardis ER, Hickenbotham M, Magrini V, Eldred J, Latreille JP, Wilson RK, Ganem D, DeRisi JL.  Viral discovery and sequence recovery using DNA microarrays. PLoS Biol. 2003 Nov;1(2):E2

Hurowitz EH, Brown PO. Genome-wide analysis of mRNA lengths in Saccharomyces cerevisiae. Genome Biol. 2003;5(1):R2

Arava Y, Wang Y, Storey JD, Liu CL, Brown PO, Herschlag D.  Genome-wide analysis of mRNA translation profiles in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A. 2003 Apr 1;100(7):3889-94

Additional Resources
Link:.

The Stanford Microarray Database (SMD)

Ramhorn is based on the open-sourced "Longhorn" codebase, which is in turn derived from SMD. 
Linux/PostgreSQL dweebs can download the Longhorn source code here.

Data: microarray images we are going to use in class
VSAAA003_532.tif
VSAAA003_635.tif

IP images, results and settings files (you will not need all of these, wait for instructions before downloading).

jdl_128_532.tif
jdl_128_635.tif
jdl_128.gpr
jdl_128.gps

jdl_132_532.tif
jdl_132_635.tif
jdl_132.gpr
jdl_132.gps

Mock IP images, results, and settings files

jdl_129_532.tif
jdl_129_635.tif
jdl_129.gpr
jdl_129.gps

jdl_131_532.tif
jdl_131_635.tif
jdl_131.gpr
jdl_131.gps

jdl_133_532.tif
jdl_133_635.tif
jdl_133.gpr
jdl_133.gps

There is no formal problem set assigned for day 1.  Instead, I will announce a typical bioinformatics problem in class in the form of a contest.
There will be a ca$h prize for the group that emails the correct answer to me first!