# HG changeset patch
# User bshanks@bshanks.dyndns.org
# Date 1240274017 25200
# Node ID 8808b945e2f721f4d137ee20e7481d3aa5b111b3
# Parent  a65f663492160539b7e4f87ebc19d63034d9dbcf
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Binary file grant.pdf has changed
--- a/grant.txt	Mon Apr 20 17:32:13 2009 -0700
+++ b/grant.txt	Mon Apr 20 17:33:37 2009 -0700
@@ -99,7 +99,7 @@
 \item Clusters: will be described later
 \end{itemize}
 
-Gene Finder is different from our Aim 1 in at least three ways. First, Gene Finder finds only single genes, whereas we will also look for combinations of genes. Second, gene finder can only use overexpression as a marker, whereas we will also search for underexpression. Third, Gene Finder uses a simple pointwise score\footnote{"Expression energy ratio", which captures overexpression.}, whereas we will also use geometric scores such as gradient similarity. Figures \ref{MOcombo}, \ref{hole}, and \ref{AUDgeometry} in Preliminary Studies section contains evidence that each of our three choices is the right one.
+Gene Finder is different from our Aim 1 in at least three ways. First, Gene Finder finds only single genes, whereas we will also look for combinations of genes. Second, gene finder can only use overexpression as a marker, whereas we will also search for underexpression. Third, Gene Finder uses a simple pointwise score\footnote{"Expression energy ratio", which captures overexpression.}, whereas we will also use geometric scores such as gradient similarity. Figures \ref{MOcombo}, \ref{hole}, and \ref{AUDgeometry} in the Preliminary Studies section contains evidence that each of our three choices is the right one.
 
 \cite{chin_genome-scale_2007} looks at the mean expression level of genes within anatomical regions, and applies a Student's t-test with Bonferroni correction to determine whether the mean expression level of a gene is significantly higher in the target region. Like AGEA, this is a pointwise measure (only the mean expression level per pixel is being analyzed), it is not being used to look for underexpression, and does not look for combinations of genes.