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human hippocampus dataset  (Spatial Transcriptomics Inc)
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Spatial Transcriptomics Inc human hippocampus dataset
a Bright-field image and manually annotated segmentation of <t>hippocampus</t> layers and white matter (WM) in the human hippocampus. b Spatial clustering of hippocampal regions using MultiGATE, SpatialGlue, and Seurat WNN. Clustering performance is assessed using the Adjusted Rand Index (ARI), with higher values indicating greater clustering accuracy. c Box plots representing attention scores for peak–gene pairs across different genomic distances, grouped based on whether they are supported by expression quantitative trait loci (eQTL) evidence. The box plots indicate the medians (centerlines), means (triangles), first and third quartiles (bounds of boxes), and 1.5 × interquartile range (whiskers). Sample sizes per bin (False/True): 0–25 kb (621/222), 25–50 kb (479/88), 50–75 kb (461/78), 75–100 kb (469/44), 100–125 kb (446/30), 125–150 kb (405/29). d Receiver operating characteristic (ROC) curves comparing the performance of MultiGATE and other methods in predicting eQTL-associated regulatory interactions. e Visualization of MultiGATE-predicted cis-regulatory interactions for the target genes CA12 and PRKD3 along with eQTL evidence. Source data are provided as a Source Data file.
Human Hippocampus Dataset, supplied by Spatial Transcriptomics Inc, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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a Bright-field image and manually annotated segmentation of hippocampus layers and white matter (WM) in the human hippocampus. b Spatial clustering of hippocampal regions using MultiGATE, SpatialGlue, and Seurat WNN. Clustering performance is assessed using the Adjusted Rand Index (ARI), with higher values indicating greater clustering accuracy. c Box plots representing attention scores for peak–gene pairs across different genomic distances, grouped based on whether they are supported by expression quantitative trait loci (eQTL) evidence. The box plots indicate the medians (centerlines), means (triangles), first and third quartiles (bounds of boxes), and 1.5 × interquartile range (whiskers). Sample sizes per bin (False/True): 0–25 kb (621/222), 25–50 kb (479/88), 50–75 kb (461/78), 75–100 kb (469/44), 100–125 kb (446/30), 125–150 kb (405/29). d Receiver operating characteristic (ROC) curves comparing the performance of MultiGATE and other methods in predicting eQTL-associated regulatory interactions. e Visualization of MultiGATE-predicted cis-regulatory interactions for the target genes CA12 and PRKD3 along with eQTL evidence. Source data are provided as a Source Data file.

Journal: Nature Communications

Article Title: MultiGATE: integrative analysis and regulatory inference in spatial multi-omics data via graph representation learning

doi: 10.1038/s41467-025-63418-x

Figure Lengend Snippet: a Bright-field image and manually annotated segmentation of hippocampus layers and white matter (WM) in the human hippocampus. b Spatial clustering of hippocampal regions using MultiGATE, SpatialGlue, and Seurat WNN. Clustering performance is assessed using the Adjusted Rand Index (ARI), with higher values indicating greater clustering accuracy. c Box plots representing attention scores for peak–gene pairs across different genomic distances, grouped based on whether they are supported by expression quantitative trait loci (eQTL) evidence. The box plots indicate the medians (centerlines), means (triangles), first and third quartiles (bounds of boxes), and 1.5 × interquartile range (whiskers). Sample sizes per bin (False/True): 0–25 kb (621/222), 25–50 kb (479/88), 50–75 kb (461/78), 75–100 kb (469/44), 100–125 kb (446/30), 125–150 kb (405/29). d Receiver operating characteristic (ROC) curves comparing the performance of MultiGATE and other methods in predicting eQTL-associated regulatory interactions. e Visualization of MultiGATE-predicted cis-regulatory interactions for the target genes CA12 and PRKD3 along with eQTL evidence. Source data are provided as a Source Data file.

Article Snippet: For the adult human hippocampus dataset (spatial ATAC–RNA–seq), the mouse brain dataset (spatial transcriptomics + metabolomics), the breast cancer-patterned spatial ATAC + RNA dataset (Supplementary Fig. ), which have ground truth spatial domain annotations, we computed the following metrics to assess clustering agreement: Rand Index (RI), ARI, Adjusted Mutual Information, Normalized Mutual Information, Homogeneity, Completeness, V-measure, Fowlkes-Mallows Index.

Techniques: Expressing