Gene expression signatures in the mammalian brain hold the key to understanding neural development and neurological diseases. MA) which displayed gene expression levels using a pseudocolor scale. The voxelation images were mapped to a 1-mm coronal slice of the mouse brain (0.02 mm bregma, 3.82 mm interaural) at the level of the striatum (10). Smoothed gene expression images were constructed using MATLAB as described previously (5C8, 22). The pixelated expression images (Fig. 2) were interpolated before their deformations onto the atlas section (21, 28). Image registration was accomplished via the thin-plate spline warping algorithm. The interpolated and deformed images were then superimposed around the atlas section (5, 7). Fig. 2 Mouse brain gene expression images. Genes were selected as having restricted expression patterns based on the microarray voxelation data. The nonradioactive in situ hybridization (ISH) images (for each gene) are reproduced with permission from the … In addition to images presented here, mirror images are shown on our voxelation website (http://vox.pharmacology.ucla.edu/home.html). These images were created by averaging the data after overlaying one hemisphere on top of the other. The resulting single hemisphere was subsequently reflected about the midline to create a full coronal image from the brain. Since each voxel now results from an averaging of six replicates, the mirror images should have decreased noise. Correlation matrix clustering Voxel voxel correlation matrices were constructed by calculating the Spearman rho correlation Mertk coefficient for each voxel (row) using all transcript or protein data to every other voxel (column) (Figs. 1, and (7 of 11), were analyzed using ImageJ (2). Coronal images were divided into seven equally thick horizontal slices. Gene expression in each slice was determined by comparing the detected signal to background. For sagittal ISH 955091-53-9 images, seven stacked equal squares were marked at the level of the striatum corresponding to the coronal section (bregma = 0.02 mm, interaural = 3.82 mm). The signal compared with background was computed for each square in the column. For the microarray voxelation, the expression for each gene was averaged across the voxels of the seven horizontal slices. Error bars (SE) reflect variation between normalized gene expression levels. Gene Ontology analysis Analysis for overrepresentation of Gene Ontology categories 955091-53-9 was conducted using EASE (14). The analysis was performed on genes with significant regional expression in the cortex, striatum, corpus callosum, and hypothalamus (Supplementary Table S2). Three GO categories, molecular function, biological process, and cellular component were used. Mass spectrometry voxelation Mass spectrometry voxelation was performed using the equivalent coronal slice of the mouse 955091-53-9 brain used for the transcriptomics as previously described (20). Briefly, 955091-53-9 a coronal section from single mouse brains were divided into 1-mm3 voxels, and each voxel was homogenized and digested into peptides using trypsin according to the previously reported protocol (27). The peptide samples from each voxel were individually analyzed by a high-throughput liquid chromatography (LC) 955091-53-9 system coupled with high-resolution Fourier transform ion cyclotron resonance (FTICR) mass spectrometer (MS). Detected LC-MS features were confidently identified as peptides by matching to a preestablished database using the accurate mass and time (AMT) tag strategy and quantified-based detected MS intensities (26). The high-throughput proteomic analyses allowed mapping of the protein abundance patterns within the coronal slice for a total of 1 1,028 proteins. URLs The primary microarray data are available at http://vox.pharmacology.ucla.edu/datadownload.html. Access to gene expression images is available from our web site at http://vox.pharmacology.ucla.edu/home.html (Supplementary Fig. S5and < 10?6) (Supplementary Fig. S1vs. (< 10?5), vs. (< 10?5), and vs. (< 10?6) (Supplementary Fig. S1, and < 10?6) (Supplementary Fig. S2< 10?6) (Supplementary Fig. S3, and gene from BGEM. An intragene scale is used, which maximizes the displayed dynamic range for each gene. Striatum-specific genes protein phosphatase 1, regulatory (inhibitor) subunit 1B (and and is likely correct and not due to background. However, the expression patterns of and show that distinguishing between the choroid plexus and dorsal.