Exploration and visualization of gene expression with neuroanatomy in the adult mouse brain-1

Olored by expression level (blue-green is low, yellow is medium, and red is high). The images at the bottom left corner show the original image data from which the data for a quadrat in the subiculum were measured along with some of the surrounding tissue. The detected signal, color mapped by expression level, is shown blended with the original image. The tick marks on the ISH image indicate 100 μm intervals, and the markings on the reference atlas Nissl sections indicate 1 cm.<p><b>Copyright information:</b></p><p>Taken from "Exploration and visualization of gene expression with neuroanatomy in the adult mouse brain"</p><p>http://www.biomedcentral.com/1471-2105/9/153</p><p>BMC Bioinformatics 2008;9():153-153.</p><p>Published online 18 Mar 2008</p><p>PMCID:PMC2375125.</p><p></p

Four genes having Teragenomics expression level 550,650 showing complex regional and cell type expression in ISH

Reference atlas annotation and corresponding Nissl for a section of the caudoputamen (CP) of the striatum. has widespread neuronal expression, while is expressed in neurons but has a strong ventral gradient in the striatum with higher expression in the nucleus accumbens (ACB) than CP. primarily labels the specific cell class oligodendrocytes and is expressed in the wall of the lateral ventricle towards the rostral migratory stream and is not expressed in the striatum .<p><b>Copyright information:</b></p><p>Taken from "Quantitative methods for genome-scale analysis of hybridization and correlation with microarray data"</p><p>http://genomebiology.com/2008/9/1/R23</p><p>Genome Biology 2008;9(1):R23-R23.</p><p>Published online 30 Jan 2008</p><p>PMCID:PMC2395252.</p><p></p

Cross-platform comparison of global dynamic range for microarray, ISH, and SAGE

Dynamic range of signal intensities in the striatum (Str; solid lines) and hypothalamus (Hyp; dashed lines) observed in GNF (green lines), Teragenomics (Tera; red lines), ABA (blue lines), and SAGE (aqua line) data sets (striatum only). The data are plotted on a log scale for 1,270 of the highest expression values. Genes on each curve are sorted independently so that only the relative range of values is preserved. The compressed dynamic range at the highest levels in ISH quantification compared to the microarray and SAGE platforms is notable.<p><b>Copyright information:</b></p><p>Taken from "Quantitative methods for genome-scale analysis of hybridization and correlation with microarray data"</p><p>http://genomebiology.com/2008/9/1/R23</p><p>Genome Biology 2008;9(1):R23-R23.</p><p>Published online 30 Jan 2008</p><p>PMCID:PMC2395252.</p><p></p

Intra- and cross-platform comparison between GNF and Teragenomics data sets for the striatum

Scatter plots showing correlation of expression levels between replicates in Teragenomics (TERA; left panel), replicates in GNF (center panel), and cross-platform for Teragenomics and GNF (right panel). Correlations and gene numbers are from Table 3. Scatter plots for the other five structures are shown in Figure S2 in Additional data file 1.<p><b>Copyright information:</b></p><p>Taken from "Quantitative methods for genome-scale analysis of hybridization and correlation with microarray data"</p><p>http://genomebiology.com/2008/9/1/R23</p><p>Genome Biology 2008;9(1):R23-R23.</p><p>Published online 30 Jan 2008</p><p>PMCID:PMC2395252.</p><p></p

Structural profile plot for expression level for six control genes, , , , , , and

Expression levels with error bars for 4 days × 4 probe measurements after three-dimensional anatomic mapping. Original ISH images at mid-sagittal plane. Segmentation expression mask of corresponding ISH sections (b) used as the basis for quantification of expression level and density. CB, cerebellum; CTX, cortex; HIP, hippocampus; HY, hypothalamus; MB, midbrain; MD, medulla; OLF, olfactory bulb; P, pons; PAL, pallidum; STR, striatum; TH, thalamus; RHP, retrohippocampal region.<p><b>Copyright information:</b></p><p>Taken from "Quantitative methods for genome-scale analysis of hybridization and correlation with microarray data"</p><p>http://genomebiology.com/2008/9/1/R23</p><p>Genome Biology 2008;9(1):R23-R23.</p><p>Published online 30 Jan 2008</p><p>PMCID:PMC2395252.</p><p></p

Structure level ratio scatter plots showing striatum (STR)/hypothalamus (HYPO), cortex (CTX)/cerebellum (CB), and CB/HYPO for ABA versus Teragenomics (TERA) and GNF versus TERA data sets

Pearson (Pr) and Spearman (Sp) correlations are shown with gene counts in parentheses. Scatter plots for the remaining structures and for ABA versus GNF are shown in Figure S4a and S4b in Additional data file 1.<p><b>Copyright information:</b></p><p>Taken from "Quantitative methods for genome-scale analysis of hybridization and correlation with microarray data"</p><p>http://genomebiology.com/2008/9/1/R23</p><p>Genome Biology 2008;9(1):R23-R23.</p><p>Published online 30 Jan 2008</p><p>PMCID:PMC2395252.</p><p></p