Large-scale mining of gene expression patterns. Paul Pavlidis [email protected] VanBUG September 2007. Students Leon French Meeta Mistry Vaneet Lotay Postdoc Jesse Gillis Undergraduates Raymond Lim Suzanne Lane Programmers Kelsey Hamer Luke McCarthy. Genome. Synapse.
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With JJ Mann, V Arango, E Sibille et al.
Data from http://national_databank.mclean.harvard.edu/
Too general, but lots of power
All mouse data sets
Mouse brain data sets
Mouse neocortex data sets
Mouse neocortex data sets examining stress
Mouse neocortex data sets examining hypoxic stress
Mouse neocortex data sets examining hypoxic stress after 3 hours of hypoxia
Very specific, low power
Array Designs: al.)178
Assays (i.e., chips): 20837
Coexpression links (probe-level): >100 million
Eisen et al., 1998 PNAS
Two ribosomal protein genes.
A simple approach:
Count Recurring patterns
Allen Brain Institute
Laurent Journot, INSERM – Universités Montpellier
Ewing et al, 2007 Molecular Systems Biology
Correlation (Global) al.)
Support (# of datasets)
Related work: Zhou XJ et al., Nat.Biotech 2005
Web-based tools for biologists; web services coming soon