MENU- THE HUMAN PROTEOME
- THE TISSUE ATLAS
- THE CELL TYPE ATLAS
- THE CELL ATLAS
- THE PATHOLOGY ATLAS
- THE BRAIN ATLAS
- THE BLOOD ATLAS
- THE METABOLIC ATLAS
- PROTEIN CLASSES
- PROTEIN EVIDENCE
T-cellsA T-cell, or T lymphocyte, is a type of white blood cell that plays a central role in cell-mediated immunity. They mature in the thymus and can be distinguished from other lymphocytes, by the presence of a T-cell receptor on the cell surface. There are several subsets of T-cells, such as cytotoxic T-cells, regulatory T-cells, helper T-cells and natural killer T-cells, with functions related to both innate and adaptive immunity. In the Blood Atlas we have 609 cell lineage enriched genes and 103 of these genes has the highest expression in blood or lymphoid tissues when comparing all tissues and organs analysed. In addition, 741 genes are cell lineage group enriched and an additional 45 genes are enhanced in this cell lineage. Altogether, 1395 genes are elevated and among these 270 also show highest expression in blood or lymphoid tissues when comparing all tissues and organs analysed.
Figure 1. The distribution of all genes across the five specificity categories based on transcript abundance in T-cell lineage as well as in the other 5 cell lineages. Table 1. Number of genes in the subdivided categories of elevated expression in T-cell lineage
Table 2. The genes with the highest level of enriched expression in T-cell lineage. "pTPM" shows the transcript level as protein-coding transcripts per million. Specificity-score corresponds to the score calculated as the fold change of T-cell lineage expression to the second highest cell lineage.
T-regsRegulatory T-cells (T-regs) has an important role in maintaining immunological tolerance, by suppressing autoreactive T-cells that have escaped negative regulation and by being involved in ending a T-cell mediated immune reaction. In the Blood Atlas we have 67 T-reg enriched genes and 19 of these genes has the highest expression in blood or lymphoid tissues when comparing all tissues and organs analysed. In addition, 163 genes are cell type group enriched and an additional 212 genes are enhanced in this cell type. Altogether, 442 genes are elevated and among these 134 also show highest expression in blood or lymphoid tissues when comparing all tissues and organs analysed. The T-regs were isolated from PBMCs. Debris and cell aggregates were eliminated based on scatter profiles. The T-reg population was sorted as CD3+/CD4+/CD127low/CD25+/CCR4+ sub-population of lymphocytes (FSClow/SSClow). 4,000 – 7,000 cells were sorted per sample for transcriptomic analysis by mRNA-sequencing. The transcriptome analysis shows that 51 % (n= 9984) of all human proteins (n=19,670) are expressed in the T-regs and 163 of these genes show an elevated expression in T-regs compared to the other 17 cell types (see figure below).
Figure 2. The distribution of all genes across the five specificity categories based on transcript abundance in T-reg cells as well as in the other 17 cell types. Table 3. Number of genes in the subdivided categories of elevated expression in T-reg cells.
Table 4. The genes with the highest level of enriched expression in T-reg cells. "pTPM" shows the transcript level as protein-coding transcripts per million. Specificity-score corresponds to the score calculated as the fold change of T-reg cell expression to the second highest cell type.
gdT-cellsGamma delta T cells (gdT-cells) are a small subset of T cells with a gamma delta T-cell receptor (TCR), instead of the common alpha beta TCR, on the cell surface. gdT-cells seem to be able to recognize whole proteins and not only peptides on the surface of antigen presenting cells, and can also specifically and rapidly respond to phosphoantigens, which is a set of nonpeptidic phosphorylated isoprenoid precursors. In the Blood Atlas we have 16 gdT-cell enriched genes and 2 of these genes has the highest expression in blood or lymphoid tissues when comparing all tissues and organs analysed. In addition, 169 genes are cell type group enriched and an additional 153 genes are enhanced in this cell type. Altogether, 338 genes are elevated and among these 88 also show highest expression in blood or lymphoid tissues when comparing all tissues and organs analysed. The gdT-cells were isolated from PBMCs. Debris and cell aggregates were eliminated based on scatter profiles. Monocytes, and B-cells were eliminated by selecting CD14neg/CD19neg/CD3+ sub-population of lymphocytes (FSClow/SSClow). The gdTCR cells were sorted as gdTCR+/TCR Vα7.2neg cells, and 5,000 – 46,000 cells were sorted per sample for transcriptomic analysis by mRNA-sequencing The transcriptome analysis shows that 53 % (n= 10383) of all human proteins (n=19,670) are expressed in the gdTCRs and 169 of these genes show an elevated expression in gdT-cells compared to the other 17 cell types (see figure below).
Figure 3. The distribution of all genes across the five specificity categories based on transcript abundance in gdT-cell cells as well as in the other 17 cell types. Table 5. Number of genes in the subdivided categories of elevated expression in gdT-cell.
Table 6. The genes with the highest level of enriched expression in gdT-cell. "pTPM" shows the transcript level as protein-coding transcripts per million. Specificity-score corresponds to the score calculated as the fold change of gdT-cell expression to the second highest cell type.
MAIT T-cellsMucosal associated invariant T-cells (MAIT T-cells) are involved in innate immunity and the defence against microbial activity and infection, but they also support the adaptive immune response and are thought to have a role in some autoimmune diseases. In the Blood Atlas we have 44 MAIT T-cell enriched genes and 8 of these genes has the highest expression in blood or lymphoid tissues when comparing all tissues and organs analysed. In addition, 167 genes are cell type group enriched and an additional 147 genes are enhanced in this cell type. Altogether, 358 genes are elevated and among these 85 also show highest expression in blood or lymphoid tissues when comparing all tissues and organs analysed. The MAIT T-cells were isolated from PBMCs. Debris and cell aggregates were eliminated by gating based on scatter profiles. Monocytes, and B-cells were eliminated by selecting CD14neg/CD19neg/CD3+ sub-population of lymphocytes (FSClow/SSClow). MAIT T-cells were sorted as gdTCRneg/TCR Vα7.2+/CD161+ cells and 3,800 – 12,000 cells were sorted per sample for transcriptomic analysis by mRNA-sequencing. The transcriptome analysis shows that 52 % (n= 10227) of all human proteins (n=19,670) are expressed in the MAIT T-cells and 167 of these genes show an elevated expression in MAIT T-cells compared to the other 17 cell types (see figure below).
Figure 4. The distribution of all genes across the five specificity categories based on transcript abundance in MAIT T-cells as well as in the other 17 cell types. Table 7. Number of genes in the subdivided categories of elevated expression in MAIT T-cells.
Table 8. The genes with the highest level of enriched expression in MAIT T-cells."pTPM" shows the transcript level as protein-coding transcripts per million. Specificity-score corresponds to the score calculated as the fold change of MAIT T-cell expression to the second highest cell type.
Naive CD4 T-cellsNaiveT-cells are located predominantly in lymphoid tissue and are mature T-cells that have not yet encountered its cognate antigen. Upon antigen activation they may further differentiate to memory T-cells. In the Blood Atlas we have 20 naive CD4 T-cell enriched genes and 3 of these genes has the highest expression in blood or lymphoid tissues when comparing all tissues and organs analysed. In addition, 158 genes are cell type group enriched and an additional 173 genes are enhanced in this cell type. Altogether, 351 genes are elevated and among these 70 also show highest expression in blood or lymphoid tissues when comparing all tissues and organs analysed. The naive CD4 T-cells were isolated from PBMCs. Debris and cell aggregates were eliminated based on scatter profiles. The naive CD4 T-cell population was sorted as CD3+/CD4+/CD8neg/CD45RA+ sub-population of lymphocytes (FSClow/SSClow). 10,000 – 77,000 cells were sorted per sample for transcriptomic analysis by mRNA-sequencing. The transcriptome analysis shows that 52 % (n= 10218) of all human proteins (n=19,670) are expressed in the naive CD4 T-cells and 158 of these genes show an elevated expression in naive CD4 T-cells compared to the other 17 cell types (see figure below).
Figure 5. The distribution of all genes across the five specificity categories based on transcript abundance in naive CD4 T-cells as well as in the other 17 cell types. Table 9. Number of genes in the subdivided categories of elevated expression in naive CD4 T-cells.
Table 10. The genes with the highest level of enriched expression in naive CD4 T-cells. "pTPM" shows the transcript level as protein-coding transcripts per million. Specificity-score corresponds to the score calculated as the fold change of naive CD4 T-cell expression to the second highest cell type.
Memory CD4 T-cellsMemory T-cells provide the immune system with an effective defence against previously encountered pathogens, by having a long lifespan and the ability to quickly expand to large numbers upon re-exposure to their cognate antigen. In the Blood Atlas we have 10 memory CD4 T-cell enriched genes and 0 of these genes has the highest expression in blood or lymphoid tissues when comparing all tissues and organs analysed. In addition, 176 genes are cell type group enriched and an additional 60 genes are enhanced in this cell type. Altogether, 246 genes are elevated and among these 60 also show highest expression in blood or lymphoid tissues when comparing all tissues and organs analysed. The memory CD4 T-cells were isolated from PBMCs. Debris and cell aggregates were eliminated based on scatter profiles. The memory CD4 T-cell population was sorted as CD3+/CD4+/CD8neg/CD45RAneg sub-population of lymphocytes (FSClow/SSClow). 10,000 – 53,000 cells were sorted per sample for transcriptomic analysis by mRNA-sequencing. The transcriptome analysis shows that 53 % (n= 10340) of all human proteins (n=19,670) are expressed in the memory CD4 T-cells and 176 of these genes show an elevated expression in memory CD4 T-cells compared to the other 17 cell types (see figure below).
Figure 6. The distribution of all genes across the five specificity categories based on transcript abundance in memory CD4 T-cells as well as in the other 17 cell types. Table 11. Number of genes in the subdivided categories of elevated expression in memory CD4 T-cells.
Table 12. The genes with the highest level of enriched expression in memory CD4 T-cells."pTPM" shows the transcript level as protein-coding transcripts per million. Specificity-score corresponds to the score calculated as the fold change of memory CD4 T-cell expression to the second highest cell type.
Naive CD8 T-cellsNaiveT-cells are located predominantly in lymphoid tissue and are mature T-cells that have not yet encountered its cognate antigen. Upon antigen activation they may further differentiate to memory T-cells. In the Blood Atlas we have 19 naive CD8 T-cell enriched genes and 1 of these genes has the highest expression in blood or lymphoid tissues when comparing all tissues and organs analysed. In addition, 195 genes are cell type group enriched and an additional 97 genes are enhanced in this cell type. Altogether, 311 genes are elevated and among these 76 also show highest expression in blood or lymphoid tissues when comparing all tissues and organs analysed. The naive CD8 T-cells were isolated from PBMCs. Debris and cell aggregates were eliminated based on scatter profiles. The naive CD8 T-cell population was sorted as CD3+/CD4neg/CD8+/CD45RA+ sub-population of lymphocytes (FSClow/SSClow). 10,000 – 77,000 cells were sorted per sample for transcriptomic analysis by mRNA-sequencing. The transcriptome analysis shows that 53 % (n= 10398) of all human proteins (n=19,670) are expressed in the naive CD8 T-cells and 195 of these genes show an elevated expression in naive CD8 T-cells compared to the other 17 cell types (see figure below).
Figure 7. The distribution of all genes across the five specificity categories based on transcript abundance in naive CD8 T-cells as well as in the other 17 cell types. Table 13. Number of genes in the subdivided categories of elevated expression in naive CD8 T-cells.
Table 14. The genes with the highest level of enriched expression in naive CD8 T-cells. "pTPM" shows the transcript level as protein-coding transcripts per million. Specificity-score corresponds to the score calculated as the fold change of naive CD8 T-cell expression to the second highest cell type.
Memory CD8 T-cellsMemory T-cells provide the immune system with an effective defence against previously encountered pathogens, by having a long lifespan and the ability to quickly expand to large numbers upon re-exposure to their cognate antigen. In the Blood Atlas we have 11 memory CD8 T-cell enriched genes and 2 of these genes has the highest expression in blood or lymphoid tissues when comparing all tissues and organs analysed. In addition, 176 genes are cell type group enriched and an additional 66 genes are enhanced in this cell type. Altogether, 253 genes are elevated and among these 82 also show highest expression in blood or lymphoid tissues when comparing all tissues and organs analysed. The memory CD8 T-cells were isolated from PBMCs. Debris and cell aggregates were eliminated based on scatter profiles. The memory CD8 T-cell population was sorted as CD3+/CD4neg/ CD8+/CD45RAneg sub-population of lymphocytes (FSClow/SSClow). 7,000 – 21,000 cells were sorted per sample for transcriptomic analysis by mRNA-sequencing. The transcriptome analysis shows that 53 % (n= 10327) of all human proteins (n=19,670) are expressed in the memory CD8 T-cells and 176 of these genes show an elevated expression in memory CD8 T-cells compared to the other 17 cell types (see figure below).
Figure 8. The distribution of all genes across the five specificity categories based on transcript abundance in memory CD8 T-cells as well as in the other 17 cell types. Table 15. Number of genes in the subdivided categories of elevated expression in memory CD8 T-cells.
Table 16. The genes with the highest level of enriched expression in memory CD8 T-cells. "pTPM" shows the transcript level as protein-coding transcripts per million. Specificity-score corresponds to the score calculated as the fold change ofmemory CD8 T-cell expression to the second highest cell type.
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The Project
The Human Protein Atlas
The Human Protein Atlas project is funded
