RNA expression in the single cell type clusters identified in this tissue visualized by a UMAP plot (top) and a bar chart (bottom).
- UMAP PLOT visualizes the cells in each cluster; where each dot corresponds to a cell. For each individual cell, mouseover reveals read count and which cluster the cell belongs to. Hovering over a cluster name will highlight the corresponding cluster in the bar chart below. There are 2 options for color schemes: 1) cell type color, which is based on cell type groups used in the Single cell type part of the Single cell resource and 2) cluster color, which assigns a unique color to each cluster.
The cells are colored according to % of max (log2(read_count+1)/log2(max(read_count)+1)*100) in five different bins (<1%,<25%,<50%,<75%,≥75%)
- The LEGEND shows RNA expression (nTPM) in each cell type cluster. Hovering over the cluster name reveals nTPM value and number of included cells. Hovering over a bar highlights the corresponding cluster in the UMAP plot above. Color-coding can be toggled on the top of the page, between 2 options: 1) cell type color, which is based on cell type groups used in the Single cell type part of the Single cell resource and 2) cluster color, which assigns a unique color to each cluster.
The plot below shows the enrichment prediction score for each cell type profiled in the tissue. This score is the mean correlation between the selected gene and the 3 reference transcripts selected to represent each cell type profiled within the tissue. An enlarged symbol indicates classification of the gene as cell type enriched in the corresponding cell type. Hover the mouse pointer over the symbols or cell type names to see the mean correlation values.
Category
Alphabetical
Enrichment
CELL TYPE MARKERSi
The heatmap in this section shows expression of the currently selected gene (on top) and well-known cell type markers in the different single cell type clusters of this tissue. The panel on the left shows which cell type each marker is associated with. Color-coding is based on cell type groups, each consisting of cell types with functional features in common.
Hover the mouse-pointer over the individual data points (squares) to see nTPM level and Z-score. Clicking on a gene name redirects to the corresponding gene page.
Z-score is when you normalize a variable such that the standard deviation is 1 and the mean is 0. Thus, all the genes are easier to compare, as they have the same center and distribution.
SINGLE CELL TYPE
BULK RNA DECONVOLUTION
Max-norm
Z-score
Fraction of highest expression (≥1 nTPM)
log2(nTPM+1) z-score
DVP - LIVERi
Relative protein amount measured using Deep Visual Proteomics. Here, on the detail page, all the biological replicates are shown, compared to the median value displayed on the gene summary page. The matched, selected single cell type clusters for the RNA-Protein comparison is also shown. The selected Cell Type clusters have the same name and ID as in the original dataset, above.
Below, we show a thumbnail overview of the tissue section used for the DVP, as well as smaller cropped area, that is clickable for a high-resolution zoomable image, where you can switch on and off the segmentation mask that was used for sample collection.
Learn more about the DVP method and different markers used the cell types here
Immunofluorescence image with DVP segmentation contours, high resolution cropped area with cell type markers (More info). This is liver, and includes a pan-Cadherin staining of hepatocytes.
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The Human Protein Atlas project is funded
