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

Journal: bioRxiv

Article Title: A high-resolution spatial map of cilia-associated proteins in the human fallopian tube

doi: 10.64898/2026.03.14.711768

Figure Lengend Snippet: The expression, functions, and characteristics of the FT-elevated transcriptome. (A) Bulk transcriptomics data of FT tissue were used to select genes with different specificity to FT based on RNA categories retrieved from the HPA. In total, 310 genes were elevated in FT and antibodies targeting 133 proteins were identified for further analysis in the current study based on stringent antibody validation criteria. (B) RNA specificity for the 310 genes elevated in FT and the tissue and cell types with the highest expression of each gene are presented in an alluvial plot (C) GO enrichment analysis for all FT-elevated genes. GO term enrichment was assessed using an over-representation test with Benjamini–Hochberg correction for multiple testing. Terms with adjusted p-values < 0.01 were considered significant.

Article Snippet: Bulk transcriptomics data, derived from the Human Protein Atlas (HPA) resource , identified 310 genes with an elevated expression in human FT compared to other tissues and organs in the human body, of which a majority were found to be associated with the structure and function of motile cilia.

Techniques: Expressing, Transcriptomics, Biomarker Discovery