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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 Immune cell section we have 460 cell lineage enriched genes and 171 of these genes has the highest expression in blood or lymphoid tissues when comparing all tissues and organs analysed. In addition, 445 genes are cell lineage group enriched and an additional 15 genes are enhanced in this cell lineage. Altogether, 920 genes are elevated and among these 275 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. "nTPM" 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 Immune cell section we have 36 T-reg 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, 223 genes are cell type group enriched and an additional 172 genes are enhanced in this cell type. Altogether, 431 genes are elevated and among these 187 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 45 % (n= 9015) of all human proteins (n=20162) are expressed in the T-regs and 223 of these genes show an elevated expression in T-regs 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 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. "nTPM" 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 Immune cell section we have 13 gdT-cell enriched genes and 5 of these genes has the highest expression in blood or lymphoid tissues when comparing all tissues and organs analysed. In addition, 141 genes are cell type group enriched and an additional 74 genes are enhanced in this cell type. Altogether, 228 genes are elevated and among these 74 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 45 % (n= 9048) of all human proteins (n=20162) are expressed in the gdTCRs and 141 of these genes show an elevated expression in gdT-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 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. "nTPM" 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 Immune cell section we have 27 MAIT 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, 154 genes are cell type group enriched and an additional 63 genes are enhanced in this cell type. Altogether, 244 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 45 % (n= 9036) of all human proteins (n=20162) are expressed in the MAIT T-cells and 154 of these genes show an elevated expression in MAIT 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 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."nTPM" 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 Immune cell section we have 1 naive 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, 204 genes are cell type group enriched and an additional 84 genes are enhanced in this cell type. Altogether, 289 genes are elevated and among these 126 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 44 % (n= 8967) of all human proteins (n=20162) are expressed in the naive CD4 T-cells and 204 of these genes show an elevated expression in naive 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 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. "nTPM" 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 Immune cell section we have 2 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, 221 genes are cell type group enriched and an additional 25 genes are enhanced in this cell type. Altogether, 248 genes are elevated and among these 122 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 45 % (n= 9085) of all human proteins (n=20162) are expressed in the memory CD4 T-cells and 221 of these genes show an elevated expression in memory CD4 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 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."nTPM" 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 Immune cell section we have 8 naive CD8 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, 241 genes are cell type group enriched and an additional 29 genes are enhanced in this cell type. Altogether, 278 genes are elevated and among these 121 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 45 % (n= 9103) of all human proteins (n=20162) are expressed in the naive CD8 T-cells and 241 of these genes show an elevated expression in naive 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 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. "nTPM" 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 Immune cell section we have 0 memory CD8 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, 230 genes are cell type group enriched and an additional 18 genes are enhanced in this cell type. Altogether, 248 genes are elevated and among these 126 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 45 % (n= 9116) of all human proteins (n=20162) are expressed in the memory CD8 T-cells and 230 of these genes show an elevated expression in memory CD8 T-cells compared to the other 17 cell types (see figure below).
Figure . 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. "nTPM" 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 Human Protein Atlas project is funded
