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

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

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

The Edinburgh Mouse Atlas Project.

<p>To link EMAP with WHS, the Waxholm volume was transformed into EMAP's native representation (b) and then mapped into EMAP Theiler Stage 23 (TS23) space, the result shown in (a). Similarly, the result of mapping the EMAP model into WHS is shown in (c). A few registration landmarks are shown in (a, b) to illustrate the process. The final transformation was established by anatomists who aligned recognizable tissue boundaries to within about five voxels in WWHS (∼100 microns). A prototype for an Edinburgh INCF hub allows access to EMAP and the related EMAGE gene expression databases available through the INCF-DAI (d). In addition to image processing–based mappings, alternative methods of mappings are being explored, including ontology-based mappings, and mapping of areas of interest across atlases using spatial rules (d).</p

Standardizing digital atlasing.

<p>The Waxholm Space (WHS) atlas acts as the hub of an infrastructure connecting data and key reference spaces. Reference atlases that have been mapped to this space are “standardized” and can be used to share their associated data and services in a manner that is meaningful to external users. Clockwise from upper left, resources may include neuroanatomic reference atlases, large-scale gene expression databases, developmental databases, MRI and DTI imaging, histological data, analysis tools, online applications, and other 3-D anatomic models.</p

The Allen Brain Atlas and Waxholm Space.

<p>(a) WHS T1 MR image sliced on orthogonal planes. Color overlay on the planes represents segmentation of WHS anatomic regions. Blue-orange-yellow overlay is an ABA gene expression correlation map (from Anatomic Gene Expression Atlas [AGEA] online application, <a href="http://mouse.brain-map.org/agea" target="_blank">http://mouse.brain-map.org/agea</a>) rendered by maximum intensity projection and showing voxels where gene expression is highly correlated with the selected point of interest (POI). This POI, in the dentate gyrus of the hippocampus, was chosen in WHS, the coordinates transformed to ABA space, the corresponding correlation volume requested from the ABA Web service. The returned volume was finally transformed back to WHS for visualization. (b) Correlation volume in (a) merged with a volume rendering of WHS cropped around the hippocampus. (c) Surface representations of hippocampus in yellow and cortex in blue show the AGEA gene expression-defined dentate gyrus in relation to an MR-defined hippocampus. (d) Top four highest correlated genes from the ABA corresponding to (c). (e) A higher resolution view of the same query within the Allen Institute Brain Explorer interface.</p

The INCF-DAI infrastructure.

<p>Individual scientific software applications will register with INCF Central for identification of file formats, transformations, standard query formats, and other essential metadata. After becoming WHS aware, key atlas hubs provide an entry point and connectivity into the community of atlases and available data resources. Presently, the Edinburgh Mouse Atlas Project (EMAP), the Whole Brain Catalog (UCSD), and the Allen Brain Atlas (ABA) have each been registered with the WHS infrastructure and can therefore initiate queries interchangeably. Other hubs can be similarly integrated and interest and resources permit.</p

The Whole Brain Catalog.

<p>From the WBC 3-DAtlas Integration Client shown in (a), a user can generate a spatial query of WHS registered atlases. A probe can be placed in the 3-D space of the viewer and WHS coordinates of the probe translated into other atlas coordinate spaces. Implemented queries include (b) CCDB-UCSD, (c) EMAP/EMAGE, and (d) AGEA/ABA, enabling a framework for interchange between these atlases.</p