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2.1 --- a/grant.html Mon Apr 20 17:11:38 2009 -0700 2.2 +++ b/grant.html Mon Apr 20 17:13:37 2009 -0700 2.3 @@ -364,8 +364,7 @@ 2.4 2.5 Figure 2: Gene Pitx2 2.6 is selectively underex- 2.7 -pressed in area SS (so- 2.8 -matosensory). We created a normalized version of the gene expression data by subtracting each gene’s mean 2.9 +pressed in area SS. We created a normalized version of the gene expression data by subtracting each gene’s mean 2.10 expression level (over all surface pixels) and dividing each gene by its standard deviation. 2.11 The features and the target area are both functions on the surface pixels. They can be referred 2.12 to as scalar fields over the space of surface pixels; alternately, they can be thought of as images 2.13 @@ -378,7 +377,7 @@ 2.14 In the Research Plan, we describe how we will automatically locate the layer depths. For 2.15 validation, we have manually demarcated the depth of the outer boundary of cortical layer 5 2.16 throughout the cortex. 2.17 - Feature selection and scoring methods 2.18 +Feature selection and scoring methods 2.19 Underexpression of a gene can serve as a marker Underexpression of a gene can sometimes serve as a marker. See, 2.20 for example, Figure 2. 2.21 Correlation Recall that the instances are surface pixels, and consider the problem of attempting to classify each instance 2.22 @@ -471,9 +470,9 @@ 2.23 2.24 Figure 5: From left to right and top to bot- 2.25 tom, single genes which roughly identify ar- 2.26 -eas SS (somatosensory primary +supplemental), 2.27 -SSs (supplemental somatosensory), PIR (piri- 2.28 -form), FRP (frontal pole), RSP (retrosplenial), 2.29 +eas SS (somatosensory primary + supplemen- 2.30 +tal), SSs (supplemental somatosensory), PIR (pir- 2.31 +iform), FRP (frontal pole), RSP (retrosplenial), 2.32 COApm (Cortical amygdalar, posterior part, me- 2.33 dial zone). Grouping some areas together, we 2.34 have also found genes to identify the groups

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5.1 --- a/grant.txt Mon Apr 20 17:11:38 2009 -0700 5.2 +++ b/grant.txt Mon Apr 20 17:13:37 2009 -0700 5.3 @@ -238,7 +238,7 @@ 5.4 \\ 5.5 \includegraphics[scale=.31]{singlegene_SS_lr_top_1_654_jet.eps}\includegraphics[scale=.31]{singlegene_SS_lr_top_2_685_jet.eps} 5.6 5.7 -\caption{Top row: Genes Nfic and A930001M12Rik are the most correlated with area SS (somatosensory cortex). Bottom row: Genes C130038G02Rik and Cacna1i are those with the best fit using logistic regression. Within each picture, the vertical axis roughly corresponds to anterior at the top and posterior at the bottom, and the horizontal axis roughly corresponds to medial at the left and lateral at the right. The red outline is the boundary of region SS. Pixels are colored according to correlation, with red meaning high correlation and blue meaning low.} 5.8 +\caption{Top row: Genes $Nfic$ and $A930001M12Rik$ are the most correlated with area SS (somatosensory cortex). Bottom row: Genes $C130038G02Rik$ and $Cacna1i$ are those with the best fit using logistic regression. Within each picture, the vertical axis roughly corresponds to anterior at the top and posterior at the bottom, and the horizontal axis roughly corresponds to medial at the left and lateral at the right. The red outline is the boundary of region SS. Pixels are colored according to correlation, with red meaning high correlation and blue meaning low.} 5.9 \label{SScorrLr}\end{wrapfigure} 5.10 5.11 5.12 @@ -266,7 +266,7 @@ 5.13 5.14 \begin{wrapfigure}{L}{0.2\textwidth}\centering 5.15 \includegraphics[scale=.31]{holeExample_2682_SS_jet.eps} 5.16 -\caption{Gene Pitx2 is selectively underexpressed in area SS.} 5.17 +\caption{Gene $Pitx2$ is selectively underexpressed in area SS.} 5.18 \label{hole}\end{wrapfigure} 5.19 5.20 5.21 @@ -358,7 +358,7 @@ 5.22 \includegraphics[scale=.31]{singlegene_example_3709_Tshz2_RSP_jet.eps}\includegraphics[scale=.31]{singlegene_example_3674_Trhr_COApm_jet.eps} 5.23 \includegraphics[scale=.31]{singlegene_example_925_Col12a1_ACA+PL+ILA+DP+ORB+MO_jet.eps}\includegraphics[scale=.31]{singlegene_example_1334_Ets1_post_lat_vis_jet.eps} 5.24 5.25 -\caption{From left to right and top to bottom, single genes which roughly identify areas SS (somatosensory primary + supplemental), SSs (supplemental somatosensory), PIR (piriform), FRP (frontal pole), RSP (retrosplenial), COApm (Cortical amygdalar, posterior part, medial zone). Grouping some areas together, we have also found genes to identify the groups ACA+PL+ILA+DP+ORB+MO (anterior cingulate, prelimbic, infralimbic, dorsal peduncular, orbital, motor), posterior and lateral visual (VISpm, VISpl, VISI, VISp; posteromedial, posterolateral, lateral, and primary visual; the posterior and lateral visual area is distinguished from its neighbors, but not from the entire rest of the cortex). The genes are $Pitx2$, $Aldh1a2$, $Ppfibp1$, $Slco1a5$, $Tshz2$, $Trhr$, $Col12a1$, $Ets1$.} 5.26 +\caption{From left to right and top to bottom, single genes which roughly identify areas SS (somatosensory primary \begin{latex}+\end{latex} supplemental), SSs (supplemental somatosensory), PIR (piriform), FRP (frontal pole), RSP (retrosplenial), COApm (Cortical amygdalar, posterior part, medial zone). Grouping some areas together, we have also found genes to identify the groups ACA+PL+ILA+DP+ORB+MO (anterior cingulate, prelimbic, infralimbic, dorsal peduncular, orbital, motor), posterior and lateral visual (VISpm, VISpl, VISI, VISp; posteromedial, posterolateral, lateral, and primary visual; the posterior and lateral visual area is distinguished from its neighbors, but not from the entire rest of the cortex). The genes are $Pitx2$, $Aldh1a2$, $Ppfibp1$, $Slco1a5$, $Tshz2$, $Trhr$, $Col12a1$, $Ets1$.} 5.27 \label{singleSoFar}\end{wrapfigure} 5.28 5.29 \vspace{0.3cm}**Areas which can be identified by single genes**