Laminar and Dorsoventral Molecular Organization of the Medial Entorhinal Cortex Revealed by Large-scale Anatomical Analysis of Gene Expression
(A) Generation of a reference image (Imref) for image warping. Images were selected (left), aligned to a template image (red dotted line) by scaling, rotation and translation (Manual Rigid Reg, centre), then registered to each other using non-linear deformation (MIRT Groupwise Reg, right). Imref was defined as the median of the resulting images (Median, right). (B) The central reference image (ImrefC, S1A Fig.). (C) Image registration reveals laminar organization of gene expression. Images show the mean pixel intensity (INT) for 1000 ABA expression images before (left) and after (right) registration of the corresponding pre-processed ISH image to ImrefC. Colors represent pixel intensity (Colormap adapted from the Matplotlib ‘jet’ colormap). White boxes outline the area corresponding to the MEC, shown at higher magnification. (D) Venn diagrams indicate the number of genes detected as expressed in the MEC using RNA-seq analysis (Ensembl v73) and/or our re-registered ABA data set. (E) 2D histogram indicating the number of genes with a particular FPKM and mINT, represented using a log scale (right). White line is the linear regression fit, which indicates that RNA-seq and ABA expression are positively correlated. Data were averaged across the dorsal and ventral region. Data with zero values are included in the first histogram bin.