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GET1
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                                          • SUMMARY

                                          • TISSUE

                                          • BRAIN

                                          • SINGLE CELL

                                          • SUBCELL

                                          • CANCER

                                          • BLOOD

                                          • CELL LINE

                                          • STRUCTURE

                                          • INTERACTION

                                          • GET1
                                          SINGLE CELL TONGUE 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 CELL TYPE MARKERS
                                          Cell types
                                          Specialized epithelial cells
                                          Squamous epithelial cells
                                          Blood and immune cells
                                          Mesenchymal cells
                                          Endothelial and mural cells
                                          Stem and proliferating cells
                                          Glial cells
                                          Glandular epithelial cells
                                          Methods
                                          TONGUE DETAIL SUMMARY
                                          Schwann cellsSuprabasal keratinocytesBasal keratinocytesVascular endothelial cellsLymphatic endothelial cellsPericytesVascular smooth muscle cellsFibroblastsMast cellsMonocytesMacrophagesT-cellsMyosatellite cells0246810nCPMGlial cellsSquamous epithelial cellsSpecialized epithelial cellsEndothelial and mural cellsMesenchymal cellsBlood and immune cellsStem and proliferating cells
                                          SINGLE CELL TYPE - TONGUEi

                                          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 20
                                          c-0 Basal keratinocytes
                                          c-1 Suprabasal keratinocytes
                                          c-2 Suprabasal keratinocytes
                                          c-3 Basal keratinocytes (TA cel
                                          c-4 Suprabasal keratinocytes
                                          c-5 Basal keratinocytes
                                          c-6 CD8+ T-cells
                                          c-7 Suprabasal keratinocytes
                                          c-8 Fibroblasts
                                          c-9 Fibroblasts
                                          c-10 CD4+ T-cells
                                          c-11 Apical keratinocytes
                                          c-12 Macrophages
                                          c-13 CD4+ T-cells
                                          c-14 Venous endothelial cells
                                          c-15 Capillary endothelial cells
                                          c-16 CD4+ T-cells
                                          c-17 Suprabasal keratinocytes
                                          c-18 Suprabasal keratinocytes
                                          c-19 Pericytes
                                          c-20 Vascular smooth muscle cell
                                          c-21 Arterial endothelial cells
                                          c-22 Mast cells
                                          c-23 Myosatellite cells
                                          c-24 Lymphatic endothelial cells
                                          c-25 Schwann cells
                                          c-26 Salivary acinar cells
                                          c-27 Neutrophils
                                          c-28 Monocytes
                                          c-29 NK-cells & T-cells
                                          c-30 B-cells
                                          c-31 Fibroblasts
                                          SINGLE CELL TYPE TABULA SAPIENS - TONGUEi

                                          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 50
                                          c-0 Epithelial cell
                                          c-1 Basal cell
                                          c-2 Immune cell
                                          c-3 Fibroblast
                                          c-4 Vein endothelial cell
                                          c-5 Pericyte cell
                                          c-6 Endothelial cell of lymphat...
                                          c-7 Endothelial cell of artery
                                          c-8 Capillary endothelial cell
                                          c-9 Tongue muscle cell
                                          c-10 Keratinocyte
                                          c-11 Schwann cell
                                          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
                                          Max-norm
                                          Z-score
                                          Fraction of highest expression (≥1 nTPM)
                                          log2(nTPM+1) z-score
                                          GET1S100BMBPMPZIVLKRT1KRT10COL17A1ITGA6TP63AQP5LTFPECAM1VWFACKR1POSTNHEY1HEY2SEMA3GCA4RGCCLYVE1PROX1PDGFRBRGS5STEAP4ACTA2CNN1MYH11COL1A1DCNFBLN2PDGFRACPA3TPSAB1TPSB2CEACAM8CSF3RCXCR2FCGR3BFCN1IL1BS100A8S100A9VCANCD14FCGR3AC1QBC1QCCD3DCD3GCD4CD8AIL7RBANK1CD19MS4A1GZMANKG7PRF1PAX7Basal keratinocytes c-0Suprabasal keratinocytes c-1Suprabasal keratinocytes c-2Basal keratinocytes c-3Suprabasal keratinocytes c-4Basal keratinocytes c-5T-cells c-6Suprabasal keratinocytes c-7Fibroblasts c-8Fibroblasts c-9T-cells c-10Suprabasal keratinocytes c-11Macrophages c-12T-cells c-13Vascular endothelial cells c-14Vascular endothelial cells c-15T-cells c-16Suprabasal keratinocytes c-17Suprabasal keratinocytes c-18Pericytes c-19Vascular smooth muscle cells c-20Vascular endothelial cells c-21Mast cells c-22Myosatellite cells c-23Lymphatic endothelial cells c-24Schwann cells c-25Salivary acinar cells c-26Neutrophils c-27Monocytes c-28NK-cells c-29B-cells c-30Fibroblasts c-31Current geneSchwann cellsSuprabasal keratinocytesBasal keratinocytesSalivary acinar cellsVascular endothelial cellsLymphatic endothelial cellsPericytesVascular smooth muscle cellsFibroblastsMast cellsNeutrophilsMonocytesMacrophagesT-cellsB-cellsNK-cellsMyosatellite cells00.250.50.751-4-2024
                                          Max-norm
                                          Z-score
                                          Fraction of highest expression (≥1 nTPM)
                                          log2(nTPM+1) z-score
                                          GET1S100BMBPMPZIVLKRT1KRT10COL17A1ITGA6TP63AQP5LTFPECAM1VWFACKR1POSTNHEY1HEY2SEMA3GCA4RGCCLYVE1PROX1PDGFRBRGS5STEAP4ACTA2CNN1MYH11COL1A1DCNFBLN2PDGFRACPA3TPSAB1TPSB2CEACAM8CSF3RCXCR2FCGR3BFCN1IL1BS100A8S100A9VCANCD14FCGR3AC1QBC1QCCD3DCD3GCD4CD8AIL7RBANK1CD19MS4A1GZMANKG7PRF1PAX7Epithelial cell c-0Basal cell c-1Immune cell c-2Fibroblast c-3Vein endothelial cell c-4Pericyte cell c-5Endothelial cell of lymphatic vessel c-6Endothelial cell of artery c-7Capillary endothelial cell c-8Tongue muscle cell c-9Keratinocyte c-10Schwann cell c-11Current geneSchwann cellsSuprabasal keratinocytesBasal keratinocytesSalivary acinar cellsVascular endothelial cellsLymphatic endothelial cellsPericytesVascular smooth muscle cellsFibroblastsMast cellsNeutrophilsMonocytesMacrophagesT-cellsB-cellsNK-cellsMyosatellite cells00.250.50.751-4-2024
                                           

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