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gene umap  (Human Protein Atlas)

 
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    Human Protein Atlas gene umap
    (A) A <t>UMAP</t> of cells. Cells are colored according to cell type. Reproduced from Progatzky et al. (2021) . (B) A UMAP of genes. Here we use the 2000 most variable genes and cluster them using the Louvain algorithm. (C) As in B with genes encoding transcription factors highlighted. (D) Gene UMAPs with genes from selected Hallmark gene sets highlighted. (E) Sankey diagram showing relationships between selected gene clusters and cell clusters. (F) <t>Gene</t> <t>UMAP</t> coloured by mean z -score for expression of each of the 2000 most variable genes in selected cell types. (G) Gene UMAP coloured by absolute value of difference of mean z -score for TCells1 and TCells2. (H) Gene UMAP coloured by mean z-score for expression of each of the 2000 most variable genes in different conditions. Here WT and KO refer to control mice Sox10CreERT2; Ifngr2fl/+ (Ifngr2CTRL) and Sox10CreERT 2; Ifngr2fl/fl (Ifngr2 Δ EGC) mice respectively. (I) Violin plot showing observed UMAP distances between ligand-receptor pairs (red), randomized ligand-receptor pairs (green), and random gene pairs (blue). (J) Violin plot showing observed UMAP distances between pairs of genes encoding members of actual IntAct complexes, in comparison to randomized distances: the UMAP distance of permuted pairs, the UMAP distance for the first gene of each pair to a randomly chosen gene, and the UMAP distance between pairs derived from randomly chosen gene sets of the same size as our subset complexes.
    Gene Umap, supplied by Human Protein Atlas, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/gene+umap/pmc12831930-10-8-20?v=Human+Protein+Atlas
    Average 86 stars, based on 1 article reviews
    gene umap - by Bioz Stars, 2026-07
    86/100 stars

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    1) Product Images from "Capturing gene–cell duality in a cat’s cradle"

    Article Title: Capturing gene–cell duality in a cat’s cradle

    Journal: Bioinformatics

    doi: 10.1093/bioinformatics/btaf681

    (A) A UMAP of cells. Cells are colored according to cell type. Reproduced from Progatzky et al. (2021) . (B) A UMAP of genes. Here we use the 2000 most variable genes and cluster them using the Louvain algorithm. (C) As in B with genes encoding transcription factors highlighted. (D) Gene UMAPs with genes from selected Hallmark gene sets highlighted. (E) Sankey diagram showing relationships between selected gene clusters and cell clusters. (F) Gene UMAP coloured by mean z -score for expression of each of the 2000 most variable genes in selected cell types. (G) Gene UMAP coloured by absolute value of difference of mean z -score for TCells1 and TCells2. (H) Gene UMAP coloured by mean z-score for expression of each of the 2000 most variable genes in different conditions. Here WT and KO refer to control mice Sox10CreERT2; Ifngr2fl/+ (Ifngr2CTRL) and Sox10CreERT 2; Ifngr2fl/fl (Ifngr2 Δ EGC) mice respectively. (I) Violin plot showing observed UMAP distances between ligand-receptor pairs (red), randomized ligand-receptor pairs (green), and random gene pairs (blue). (J) Violin plot showing observed UMAP distances between pairs of genes encoding members of actual IntAct complexes, in comparison to randomized distances: the UMAP distance of permuted pairs, the UMAP distance for the first gene of each pair to a randomly chosen gene, and the UMAP distance between pairs derived from randomly chosen gene sets of the same size as our subset complexes.
    Figure Legend Snippet: (A) A UMAP of cells. Cells are colored according to cell type. Reproduced from Progatzky et al. (2021) . (B) A UMAP of genes. Here we use the 2000 most variable genes and cluster them using the Louvain algorithm. (C) As in B with genes encoding transcription factors highlighted. (D) Gene UMAPs with genes from selected Hallmark gene sets highlighted. (E) Sankey diagram showing relationships between selected gene clusters and cell clusters. (F) Gene UMAP coloured by mean z -score for expression of each of the 2000 most variable genes in selected cell types. (G) Gene UMAP coloured by absolute value of difference of mean z -score for TCells1 and TCells2. (H) Gene UMAP coloured by mean z-score for expression of each of the 2000 most variable genes in different conditions. Here WT and KO refer to control mice Sox10CreERT2; Ifngr2fl/+ (Ifngr2CTRL) and Sox10CreERT 2; Ifngr2fl/fl (Ifngr2 Δ EGC) mice respectively. (I) Violin plot showing observed UMAP distances between ligand-receptor pairs (red), randomized ligand-receptor pairs (green), and random gene pairs (blue). (J) Violin plot showing observed UMAP distances between pairs of genes encoding members of actual IntAct complexes, in comparison to randomized distances: the UMAP distance of permuted pairs, the UMAP distance for the first gene of each pair to a randomly chosen gene, and the UMAP distance between pairs derived from randomly chosen gene sets of the same size as our subset complexes.

    Techniques Used: Expressing, Control, Comparison, Derivative Assay



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    (A) A <t>UMAP</t> of cells. Cells are colored according to cell type. Reproduced from Progatzky et al. (2021) . (B) A UMAP of genes. Here we use the 2000 most variable genes and cluster them using the Louvain algorithm. (C) As in B with genes encoding transcription factors highlighted. (D) Gene UMAPs with genes from selected Hallmark gene sets highlighted. (E) Sankey diagram showing relationships between selected gene clusters and cell clusters. (F) <t>Gene</t> <t>UMAP</t> coloured by mean z -score for expression of each of the 2000 most variable genes in selected cell types. (G) Gene UMAP coloured by absolute value of difference of mean z -score for TCells1 and TCells2. (H) Gene UMAP coloured by mean z-score for expression of each of the 2000 most variable genes in different conditions. Here WT and KO refer to control mice Sox10CreERT2; Ifngr2fl/+ (Ifngr2CTRL) and Sox10CreERT 2; Ifngr2fl/fl (Ifngr2 Δ EGC) mice respectively. (I) Violin plot showing observed UMAP distances between ligand-receptor pairs (red), randomized ligand-receptor pairs (green), and random gene pairs (blue). (J) Violin plot showing observed UMAP distances between pairs of genes encoding members of actual IntAct complexes, in comparison to randomized distances: the UMAP distance of permuted pairs, the UMAP distance for the first gene of each pair to a randomly chosen gene, and the UMAP distance between pairs derived from randomly chosen gene sets of the same size as our subset complexes.
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    (A) A <t>UMAP</t> of cells. Cells are colored according to cell type. Reproduced from Progatzky et al. (2021) . (B) A UMAP of genes. Here we use the 2000 most variable genes and cluster them using the Louvain algorithm. (C) As in B with genes encoding transcription factors highlighted. (D) Gene UMAPs with genes from selected Hallmark gene sets highlighted. (E) Sankey diagram showing relationships between selected gene clusters and cell clusters. (F) <t>Gene</t> <t>UMAP</t> coloured by mean z -score for expression of each of the 2000 most variable genes in selected cell types. (G) Gene UMAP coloured by absolute value of difference of mean z -score for TCells1 and TCells2. (H) Gene UMAP coloured by mean z-score for expression of each of the 2000 most variable genes in different conditions. Here WT and KO refer to control mice Sox10CreERT2; Ifngr2fl/+ (Ifngr2CTRL) and Sox10CreERT 2; Ifngr2fl/fl (Ifngr2 Δ EGC) mice respectively. (I) Violin plot showing observed UMAP distances between ligand-receptor pairs (red), randomized ligand-receptor pairs (green), and random gene pairs (blue). (J) Violin plot showing observed UMAP distances between pairs of genes encoding members of actual IntAct complexes, in comparison to randomized distances: the UMAP distance of permuted pairs, the UMAP distance for the first gene of each pair to a randomly chosen gene, and the UMAP distance between pairs derived from randomly chosen gene sets of the same size as our subset complexes.
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    (A) A <t>UMAP</t> of cells. Cells are colored according to cell type. Reproduced from Progatzky et al. (2021) . (B) A UMAP of genes. Here we use the 2000 most variable genes and cluster them using the Louvain algorithm. (C) As in B with genes encoding transcription factors highlighted. (D) Gene UMAPs with genes from selected Hallmark gene sets highlighted. (E) Sankey diagram showing relationships between selected gene clusters and cell clusters. (F) <t>Gene</t> <t>UMAP</t> coloured by mean z -score for expression of each of the 2000 most variable genes in selected cell types. (G) Gene UMAP coloured by absolute value of difference of mean z -score for TCells1 and TCells2. (H) Gene UMAP coloured by mean z-score for expression of each of the 2000 most variable genes in different conditions. Here WT and KO refer to control mice Sox10CreERT2; Ifngr2fl/+ (Ifngr2CTRL) and Sox10CreERT 2; Ifngr2fl/fl (Ifngr2 Δ EGC) mice respectively. (I) Violin plot showing observed UMAP distances between ligand-receptor pairs (red), randomized ligand-receptor pairs (green), and random gene pairs (blue). (J) Violin plot showing observed UMAP distances between pairs of genes encoding members of actual IntAct complexes, in comparison to randomized distances: the UMAP distance of permuted pairs, the UMAP distance for the first gene of each pair to a randomly chosen gene, and the UMAP distance between pairs derived from randomly chosen gene sets of the same size as our subset complexes.
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    (A) A <t>UMAP</t> of cells. Cells are colored according to cell type. Reproduced from Progatzky et al. (2021) . (B) A UMAP of genes. Here we use the 2000 most variable genes and cluster them using the Louvain algorithm. (C) As in B with genes encoding transcription factors highlighted. (D) Gene UMAPs with genes from selected Hallmark gene sets highlighted. (E) Sankey diagram showing relationships between selected gene clusters and cell clusters. (F) <t>Gene</t> <t>UMAP</t> coloured by mean z -score for expression of each of the 2000 most variable genes in selected cell types. (G) Gene UMAP coloured by absolute value of difference of mean z -score for TCells1 and TCells2. (H) Gene UMAP coloured by mean z-score for expression of each of the 2000 most variable genes in different conditions. Here WT and KO refer to control mice Sox10CreERT2; Ifngr2fl/+ (Ifngr2CTRL) and Sox10CreERT 2; Ifngr2fl/fl (Ifngr2 Δ EGC) mice respectively. (I) Violin plot showing observed UMAP distances between ligand-receptor pairs (red), randomized ligand-receptor pairs (green), and random gene pairs (blue). (J) Violin plot showing observed UMAP distances between pairs of genes encoding members of actual IntAct complexes, in comparison to randomized distances: the UMAP distance of permuted pairs, the UMAP distance for the first gene of each pair to a randomly chosen gene, and the UMAP distance between pairs derived from randomly chosen gene sets of the same size as our subset complexes.
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    Image Search Results


    (A) A UMAP of cells. Cells are colored according to cell type. Reproduced from Progatzky et al. (2021) . (B) A UMAP of genes. Here we use the 2000 most variable genes and cluster them using the Louvain algorithm. (C) As in B with genes encoding transcription factors highlighted. (D) Gene UMAPs with genes from selected Hallmark gene sets highlighted. (E) Sankey diagram showing relationships between selected gene clusters and cell clusters. (F) Gene UMAP coloured by mean z -score for expression of each of the 2000 most variable genes in selected cell types. (G) Gene UMAP coloured by absolute value of difference of mean z -score for TCells1 and TCells2. (H) Gene UMAP coloured by mean z-score for expression of each of the 2000 most variable genes in different conditions. Here WT and KO refer to control mice Sox10CreERT2; Ifngr2fl/+ (Ifngr2CTRL) and Sox10CreERT 2; Ifngr2fl/fl (Ifngr2 Δ EGC) mice respectively. (I) Violin plot showing observed UMAP distances between ligand-receptor pairs (red), randomized ligand-receptor pairs (green), and random gene pairs (blue). (J) Violin plot showing observed UMAP distances between pairs of genes encoding members of actual IntAct complexes, in comparison to randomized distances: the UMAP distance of permuted pairs, the UMAP distance for the first gene of each pair to a randomly chosen gene, and the UMAP distance between pairs derived from randomly chosen gene sets of the same size as our subset complexes.

    Journal: Bioinformatics

    Article Title: Capturing gene–cell duality in a cat’s cradle

    doi: 10.1093/bioinformatics/btaf681

    Figure Lengend Snippet: (A) A UMAP of cells. Cells are colored according to cell type. Reproduced from Progatzky et al. (2021) . (B) A UMAP of genes. Here we use the 2000 most variable genes and cluster them using the Louvain algorithm. (C) As in B with genes encoding transcription factors highlighted. (D) Gene UMAPs with genes from selected Hallmark gene sets highlighted. (E) Sankey diagram showing relationships between selected gene clusters and cell clusters. (F) Gene UMAP coloured by mean z -score for expression of each of the 2000 most variable genes in selected cell types. (G) Gene UMAP coloured by absolute value of difference of mean z -score for TCells1 and TCells2. (H) Gene UMAP coloured by mean z-score for expression of each of the 2000 most variable genes in different conditions. Here WT and KO refer to control mice Sox10CreERT2; Ifngr2fl/+ (Ifngr2CTRL) and Sox10CreERT 2; Ifngr2fl/fl (Ifngr2 Δ EGC) mice respectively. (I) Violin plot showing observed UMAP distances between ligand-receptor pairs (red), randomized ligand-receptor pairs (green), and random gene pairs (blue). (J) Violin plot showing observed UMAP distances between pairs of genes encoding members of actual IntAct complexes, in comparison to randomized distances: the UMAP distance of permuted pairs, the UMAP distance for the first gene of each pair to a randomly chosen gene, and the UMAP distance between pairs derived from randomly chosen gene sets of the same size as our subset complexes.

    Article Snippet: Relationships between genes can be displayed on a gene UMAP (this idea was independently arrived at and exploited in The Human Protein Atlas—proteinatlas.org).

    Techniques: Expressing, Control, Comparison, Derivative Assay