Details
The data is based on The Human Protein Atlas version 23.0 and Ensembl version 109.
Each dataset in the UMAP coordinates for cells is an
Association of the form
<|cluster id1 → {{cell id11, {UMAP_x11, UMAP_y11}}, {cell id12, {UMAP_x12, UMAP_y12}}, …, {cell id1N, {UMAP_x1N, UMAP_y1N}}}, …, cluster idM → {{cell idM1, {UMAP_xM1, UMAP_yM1}}, {cell idM2, {UMAP_xM2, UMAP_yM2}}, …, {cell idMK, {UMAP_xMK, UMAP_yMK}}}|>, where M, N, K are positive integers.
Uniform Manifold Approximation and Projection (UMAP) is a method for reducing the dimensionality of a data set (
Becht E et al. (2018))
Gene and protein expression levels for different datasets are expressed as transcripts per million ("TPM"), protein-transcripts per million ("pTPM") and normalized expression ("nTPM").
The default content is a
Association containing a the expression levels (nTPM) of genes in different human tissues along with these additional data:
"TissueAtlas Gene co-expression network" | list of gene pairs with high correlation (>0.7) in expression in tissues |
"TissueAtlas Gene co-expression graph" | graph of co-expressing genes in tissues |
"TissueAtlas Gene co-expression network Graph measures" | graph measures for the "TissueAtlas Gene co-expression network" |
"TissueAtlas maximum expression location" | maximum expression location of genes |
"BrainAtlas gene expression (TPM)" | expression levels (TPM) of genes in human brain |
"BrainAtlas gene expression (pTPM)" | expression levels (pTPM) of genes in human brain |
"BrainAtlas gene expression (nTPM)" | expression levels (nTPM) of genes in human brain |
"BrainAtlas Gene co-expression network" | list of gene pairs with high correlation (>0.7) in expression in human brain |
"BrainAtlas Gene co-expression graph" | graph of co-expressing genes in human brain |
"BrainAtlas Gene co-expression network Graph measures" | graph measures for the "BrainAtlas Gene co-expression network" |
"PathologyAtlas" | data about roles of genes in different cancers |
"PathologyAtlas mRNA expression (FPKM) "<>cancer | gene expression (FPKM) values for different genes in different cancer types |
"PathologyAtlas Samples" | sample details for gene expression data in different cancers |
"SingleCellAtlas expression (nTPM)" | expression levels (nTPM) of genes in different cell types |
"SingleCellAtlas cell clusters" | description of cell clusters |
"SingleCellAtlas expression in cell clusters(nTPM)" | expression levels (nTPM) of genes in different cell types and clusters |
"SingleCellAtlas Gene co-expression network" | list of gene pairs with high correlation (>0.7) in expression in single cell types |
"SingleCellAtlas Gene co-expression graph" | graph of co-expressing genes in different human single cell types |
"SingleCellAtlas Gene co-expression network Graph measures" | graph measures for the "SingleCellAtlas Gene co-expression network" |
"SingleCellAtlas UMAP coordinates in tissue "<>tissue | UMAP coordinates for cells in clusters for different tissues |
"SubCellularAtlas" | expression of genes in different subcellular regions |
"Ensembl ID gene name association" | Association of Emsembl IDs of genes and common gene names |
"Ensembl ID gene description UniProtID association" | Association of Emsembl IDs of genes to gene description and UniProtID |
"Organ tissue association" | Association of organs and tissues belonging to an organ |
"PathologyAtlas mRNA expression (FPKM) "<>cancer has the gene expression (FPKM) values for different genes in different cancer types for different samples in The Cancer Genome Atlas.
cancer has the following values: "BRCA","BLCA","CESC","COAD","READ","GBM","HNSC","KIRC","KIRP","KICH","LIHC","LUAD","LUSC","OV","PAAD","PRAD","SKCM","STAD","TGCT","THCA","UCEC". These are abbreviations for different cancer types
tissue for UMAP coordinates can be adipose_tissue, bone_marrow, brain, breast, bronchus, colon, endometrium, esophagus, eye, fallopian_tube, heart_muscle, kidney, liver, lung, lymph_node, ovary, pancreas, pbmc, placenta, prostate, rectum, salivary_gland, skeletal_muscle, skin, small_intestine, spleen, stomach, testis, thymus, tongue and vascular.