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Non-standard applications of DNA microarrays - "ChiP on chip" and BioProspector
Time: Thursday, August 5, 9:00 am - noon
Place: Bioinformatics Computer Core Lab (Rm 104), Life Sciences Bldg
Organizers:
Paul Fawcett
Audience: Primarily 1st year students
Topics of 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 of 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
Data: - the primary data we will be using today will the files we created on
day 1 using the Ramhorn Array Database.
Before coming to the session
- Look over the above articles if you haven't already.
- 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.
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