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GET1
HPA
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                                          • SUMMARY

                                          • TISSUE

                                          • BRAIN

                                          • SINGLE CELL

                                          • SUBCELL

                                          • CANCER

                                          • BLOOD

                                          • CELL LINE

                                          • STRUCTURE

                                          • INTERACTION

                                          • GET1
                                          SINGLE CELL SPLEEN Show tissue menu
                                          ADIPOSE TISSUE ADRENAL GLAND BLOOD BONE MARROW BRAIN BREAST COLON ENDOMETRIUM EPIDIDYMIS ESOPHAGUS
                                          EYE FALLOPIAN TUBE HEART MUSCLE KIDNEY LIVER LUNG LYMPH NODE OVARY PANCREAS PITUITARY GLAND
                                          PLACENTA PROSTATE RECTUM SALIVARY GLAND SKELETAL MUSCLE SKIN SMALL INTESTINE SPLEEN STOMACH TESTIS
                                          THYMUS THYROID GLAND TONGUE URINARY BLADDER VASCULATURE
                                          Single cell type
                                          Tabula sapiens
                                          Tissue cell type
                                          SINGLE CELL TYPE TABULA SAPIENS TISSUE CELL TYPE CELL TYPE MARKERS
                                          Cell types
                                          Blood and immune cells
                                          Endothelial and mural cells
                                          Methods
                                          Cell type enrichment
                                          Spleen
                                          Methods
                                          SPLEEN DETAIL SUMMARY
                                          Lymphatic endothelial cellsNeutrophil progenitorsNeutrophilsMonocytesMacrophagesT-cellsInnate lymphoid cellsB-cellsPlasma cellsNK-cellsPlateletsErythrocytes0246810nCPMEndothelial and mural cellsBlood and immune cells
                                          SINGLE CELL TYPE - SPLEENi

                                          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.

                                          Cell type color
                                          Cluster color
                                          Colored according to cell type group
                                          Colored according to clusters
                                          Read count filter: 0
                                          Cluster filter:
                                           
                                          Cluster Cell type Expression (nCPM)
                                          0 10
                                          c-0 Neutrophils
                                          c-1 B-cells
                                          c-2 Neutrophils
                                          c-3 CD8+ T-cells
                                          c-4 NK-cells
                                          c-5 CD4+ T-cells
                                          c-6 Monocytes
                                          c-7 B-cells
                                          c-8 Monocytes
                                          c-9 CD8+ T-cells
                                          c-10 Plasma cells
                                          c-11 CD8+ T-cells
                                          c-12 Macrophages
                                          c-13 B-cells
                                          c-14 Lymphatic endothelial cells
                                          c-15 NK-cells
                                          c-16 Myelocytes
                                          c-17 Erythrocytes
                                          c-18 Platelets
                                          c-19 CD8+ T-cells
                                          c-20 Innate lymphoid cells
                                          c-21 Vascular smooth muscle cell
                                          SINGLE CELL TYPE TABULA SAPIENS - SPLEENi

                                          RNA expression in the single cell type clusters identified in this tissue visualized by a UMAP plot and a bar chart. This window shows single cell expression data generated by the https://tabula-sapiens.sf.czbiohub.org/about#consortium, that also offers UMAP visualization and cell type clusters for each tissue sample: https://tabula-sapiens.sf.czbiohub.org/organs, here integrate offering easy comparison to the HPA cluster method of single cell types.

                                          • 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.

                                          Cell type color
                                          Cluster color
                                          Colored according to cell type group
                                          Colored according to clusters
                                          Read count filter: 0
                                           
                                          Cluster Cell type Expression (nCPM)
                                          0 2810
                                          c-0 Cd8-positive, alpha-beta me...
                                          c-1 Macrophage
                                          c-2 Naive thymus-derived cd4-po...
                                          c-3 Intermediate monocyte
                                          c-4 Endothelial cell
                                          c-5 Memory b cell
                                          c-6 Classical monocyte
                                          c-7 Neutrophil
                                          c-8 Naive b cell
                                          c-9 Plasma cell
                                          c-10 Cd4-positive, alpha-beta me...
                                          c-11 Type i nk t cell
                                          c-12 Naive thymus-derived cd8-po...
                                          c-13 Nk cell
                                          c-14 Innate lymphoid cell
                                          c-15 Erythrocyte
                                          c-16 Regulatory t cell
                                          c-17 Platelet
                                          c-18 Hematopoietic stem cell
                                          c-19 Cd141-positive myeloid dend...
                                          c-20 Cd1c-positive myeloid dendr...
                                          c-21 Plasmacytoid dendritic cell
                                          c-22 Mature nk t cell
                                          c-23 Cd8-positive, alpha-beta t ...
                                          TISSUE CELL TYPE - SPLEENi

                                          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
                                          Fibroblasts_1Fibroblasts_2Mitotic cells (Spleen)ErythrocytesB-cells (Spleen)NK-cells (Spleen)Endothelial cellsSmooth muscle cellsMacrophagesNeutrophils_1Neutrophils_2T-cellsPlasma cells0.30.40.50.60.70.80.91.0EnrichmentMesenchymal cellsStem and proliferating cellsBlood and immune cellsEndothelial and mural cellsMuscle cells
                                          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
                                          TABULA SAPIENS
                                          TISSUE CELL TYPE
                                          Max-norm
                                          Z-score
                                          Fraction of highest expression (≥1 nTPM)
                                          log2(nTPM+1) z-score
                                          GET1LYVE1PROX1PDGFRBRGS5STEAP4ACTA2CNN1MYH11CAMPCEACAM8LTFCSF3RCXCR2FCGR3BFCN1IL1BS100A8S100A9VCANCD14C1QBC1QCHLA-DRAHLA-DRB1F13A1CD3DCD3GCD4CD8AIL7RGATA3HPGDSIL9RNCR2RORCBANK1CD19MS4A1DERL3IGHA1GZMANKG7PRF1GP1BAPPBPHBA1HBBNeutrophils c-0B-cells c-1Neutrophils c-2T-cells c-3NK-cells c-4T-cells c-5Monocytes c-6B-cells c-7Monocytes c-8T-cells c-9Plasma cells c-10T-cells c-11Macrophages c-12B-cells c-13Lymphatic endothelial cells c-14NK-cells c-15Neutrophil progenitors c-16Erythrocytes c-17Platelets c-18T-cells c-19Innate lymphoid cells c-20Mural cells c-21Current geneLymphatic endothelial cellsPericytesVascular smooth muscle cellsNeutrophil progenitorsNeutrophilsMonocytesMacrophagesT-cellsInnate lymphoid cellsB-cellsPlasma cellsNK-cellsPlateletsErythrocytes00.250.50.751-4-2024
                                          Max-norm
                                          Z-score
                                          Fraction of highest expression (≥1 nTPM)
                                          log2(nTPM+1) z-score
                                          GET1LYVE1PROX1PDGFRBRGS5STEAP4ACTA2CNN1MYH11CAMPCEACAM8LTFCSF3RCXCR2FCGR3BFCN1IL1BS100A8S100A9VCANCD14C1QBC1QCHLA-DRAHLA-DRB1F13A1CD3DCD3GCD4CD8AIL7RGATA3HPGDSIL9RNCR2RORCBANK1CD19MS4A1DERL3IGHA1GZMANKG7PRF1GP1BAPPBPHBA1HBBCd8-positive, alpha-beta memory t cell c-0Macrophage c-1Naive thymus-derived cd4-positive, alpha-beta t cell c-2Intermediate monocyte c-3Endothelial cell c-4Memory b cell c-5Classical monocyte c-6Neutrophil c-7Naive b cell c-8Plasma cell c-9Cd4-positive, alpha-beta memory t cell c-10Type i nk t cell c-11Naive thymus-derived cd8-positive, alpha-beta t cell c-12Nk cell c-13Innate lymphoid cell c-14Erythrocyte c-15Regulatory t cell c-16Platelet c-17Hematopoietic stem cell c-18Cd141-positive myeloid dendritic cell c-19Cd1c-positive myeloid dendritic cell c-20Plasmacytoid dendritic cell c-21Mature nk t cell c-22Cd8-positive, alpha-beta t cell c-23Current geneLymphatic endothelial cellsPericytesVascular smooth muscle cellsNeutrophil progenitorsNeutrophilsMonocytesMacrophagesT-cellsInnate lymphoid cellsB-cellsPlasma cellsNK-cellsPlateletsErythrocytes00.250.50.751-4-2024
                                          GET1 CCDC80COL3A1GPX8ANGPTL1C7MMP2CENPFMKI67TOP2AAHSPALAS2SLC4A1CD19MS4A1TNFRSF13CKLRF1NCR1SH2D1BERGFGD5PPFIBP1ACTG2CNN1DESC1QCCD68FCGR3AELANEMPOPRTN3AQP9CSF3RMMP25CD3DTRACTRBC1IGKCIGLC2JCHAINCCDC80COL3A1GPX8ANGPTL1C7MMP2CENPFMKI67TOP2AAHSPALAS2SLC4A1CD19MS4A1TNFRSF13CKLRF1NCR1SH2D1BERGFGD5PPFIBP1ACTG2CNN1DESC1QCCD68FCGR3AELANEMPOPRTN3AQP9CSF3RMMP25CD3DTRACTRBC1IGKCIGLC2JCHAINCurrent geneFibroblasts_1Fibroblasts_2Mitotic cells (Spleen)ErythrocytesB-cells (Spleen)NK-cells (Spleen)Endothelial cellsSmooth muscle cellsMacrophagesNeutrophils_1Neutrophils_2T-cellsPlasma cells<00.250.50.751
                                           

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