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Fig. 4 | Genome Biology

Fig. 4

From: SPARK-X: non-parametric modeling enables scalable and robust detection of spatial expression patterns for large spatial transcriptomic studies

Fig. 4

Analyzing mouse olfactory bulb HDST data. A H&E image of mouse olfactory bulb (left panel) and matching morphological annotation (middle panel) in the HDST data. Spots are colored by morphological layer shown in the legend (right panel), where the layer annotations were from ref [15]. H&E image reproduced from ref. [15] with permission. B Visualization of three representative SE genes identified only by SPARK-X in the HDST data. The top panels show in situ hybridization of the three genes obtained from the Allen Brain Atlas. The bottom panels show spatial expression patterns of the three genes at single-cell-level resolution (green, high expression; antique-white, low expression). P values from SPARK-X are shown inside parentheses. C Heatmap shows expression level of 125 SE genes (columns) across eight major morphological layers (rows). Colored bar at the bottom represents five gene clusters. RMS, rostral migratory system; E, ependymal cell zone; GCL, granule cell layer; IPL, internal plexiform layer; M/T, mitral layer; EPL, external plexiform layer; GL, glomerular layer; ONL, olfactory nerve layer

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