Research Simulation
Non-standard applications of DNA microarrays - "ChiP on chip" and BioProspector
(August 5)

Time: Wed-Thu, August 5, 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

Microarrays for diagnostics
Microarrays as a measure of spatial segregation of macromolecules in the cell
Virtual Northern blots with microarrays
Studying translation with microarrays
Array comparative genome hybridization
Tissue microarrays
"ChIP on chip"

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

Links:

The BioProspector web site.
The web supplement for the Lieb Rap1 paper.
List of previously known Rap1 targets.

The primary data we will be using today will the files we created on day 1 using the Ramhorn Array Database.

The problem set will be in class, and based on actual microarray data from the Lieb paper.  We will see if we can succesfully  "discover" the binding site of the yeast Rap1 transcription factor using the combination of microarrays and bioinformatics.