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Cited by 331Gene expression and cancer classificationBioinformatics and Genomic NetworksT-cell and B-cell Immunology

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Cell-type specific gene expression profiles of leukocytes in human peripheral blood

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Palmer, Chana, Diehn, Maximilian, Alizadeh, Ash A, Brown, Patrick O·2006·BMC Genomics
DOI 10.1186/1471-2164-7-115PMC PMC1479811
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Abstract

Background: Blood is a complex tissue comprising numerous cell types with distinct functions and corresponding gene expression profiles. We attempted to define the cell type specific gene expression patterns for the major constituent cells of blood, including B-cells, CD4+ T-cells, CD8+ T-cells, lymphocytes and granulocytes. We did this by comparing the global gene expression profiles of purified B-cells, CD4+ T-cells, CD8+ T-cells, granulocytes, and lymphocytes using cDNA microarrays. Results: Unsupervised clustering analysis showed that similar cell populations from different donors share common gene expression profiles. Supervised analyses identified gene expression signatures for B-cells (427 genes), T-cells (222 genes), CD8+ T-cells (23 genes), granulocytes (411 genes), and lymphocytes (67 genes). No statistically significant gene expression signature was identified for CD4+ cells. Genes encoding cell surface proteins were disproportionately represented among the genes that distinguished among the lymphocyte subpopulations. Lymphocytes were distinguishable from granulocytes based on their higher levels of expression of genes encoding ribosomal proteins, while granulocytes exhibited characteristic expression of various cell surface and inflammatory proteins. Conclusion: The genes comprising the cell-type specific signatures encompassed many of the genes already known to be involved in cell-type specific processes, and provided clues that may prove useful in discovering the functions of many still unannotated genes. The most prominent feature of the cell type signature genes was the enrichment of genes encoding cell surface proteins, perhaps reflecting the importance of specialized systems for sensing the environment to the physiology of resting leukocytes.

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Figure 1 Overview of hierarchical clustering of all samples. Hierarchically clustered gene expression profiles of 28 mixed and purified leukocyte samples. Results for ~741 genes with high variation in transcript levels among these samples. Genes and blood samples are organized by hierarchical clustering based on overall similarity in expression patterns. Expression levels are represented by a color key in which bright red represents the highest levels and bright green represents the lowest levels, and less saturated shades represent intermediate levels of expression. Values were centered across all samples to a mean of zero. Clusters of genes are labeled according to which samples have the highest relative gene expression.
Figure 1 Overview of hierarchical clustering of all samples. Hierarchically clustered gene expression profiles of 28 mixed and purified leukocyte samples. Results for ~741 genes with high variation in transcript levels among these samples. Genes and blood samples are organized by hierarchical clustering based on overall similarity in expression patterns. Expression levels are represented by a color key in which bright red represents the highest levels and bright green represents the lowest levels, and less saturated shades represent intermediate levels of expression. Values were centered across all samples to a mean of zero. Clusters of genes are labeled according to which samples have the highest relative gene expression.CC BY · PubMed Central
Figure 2 B-cell signature genes. Relative expression of B-cell signature genes is shown for all samples. Genes (rows) are sorted in descending order of correlation of gene expression with relative abundance of B-cells. Samples (columns) are ordered in decreasing order of estimated relative abundance of B-cells from left to right. The grayscale bar on top shows the estimated relative abundance of B-cells in each class of samples – black indicates 100% relative abundance of B-cells, white indicates 0% relative abundance of B-cells, and grey indicates intermediate relative abundance of B-cells. Gene expression values are centered across all samples to a median of zero. All genes mentioned in the text are listed in order of correlation with B-cell abundance and black bars indicate their positions in the figure.
Figure 2 B-cell signature genes. Relative expression of B-cell signature genes is shown for all samples. Genes (rows) are sorted in descending order of correlation of gene expression with relative abundance of B-cells. Samples (columns) are ordered in decreasing order of estimated relative abundance of B-cells from left to right. The grayscale bar on top shows the estimated relative abundance of B-cells in each class of samples – black indicates 100% relative abundance of B-cells, white indicates 0% relative abundance of B-cells, and grey indicates intermediate relative abundance of B-cells. Gene expression values are centered across all samples to a median of zero. All genes mentioned in the text are listed in order of correlation with B-cell abundance and black bars indicate their positions in the figure.CC BY · PubMed Central
Figure 3 T-cell signature genes. Relative expression of T-cell signature genes is shown for all samples. Genes (rows) are sorted in descending order of correlation of gene expression with relative abundance of T-cells. Samples (columns) are ordered in decreasing relative abundance from left to right. Gene expression values are centered across all samples to a median of zero. The grayscale bar on top shows the estimated relative abundance of T-cells in each class of samples – black indicates 100% relative abundance of T-cells, white indicates 0% relative abundance of T-cells, and grey indicates intermediate relative abundance of T-cells. All genes mentioned in the text are listed in order of correlation with T-cell abundance, and black bars indicate their positions in the figure.
Figure 3 T-cell signature genes. Relative expression of T-cell signature genes is shown for all samples. Genes (rows) are sorted in descending order of correlation of gene expression with relative abundance of T-cells. Samples (columns) are ordered in decreasing relative abundance from left to right. Gene expression values are centered across all samples to a median of zero. The grayscale bar on top shows the estimated relative abundance of T-cells in each class of samples – black indicates 100% relative abundance of T-cells, white indicates 0% relative abundance of T-cells, and grey indicates intermediate relative abundance of T-cells. All genes mentioned in the text are listed in order of correlation with T-cell abundance, and black bars indicate their positions in the figure.CC BY · PubMed Central
Figure 4 CD8+ T-cell signature genes. Relative expression of CD8+ T-cell signature genes is shown for all samples. Genes (rows) are sorted in descending order of correlation of gene expression with relative abundance of T-cells. Samples (columns) are ordered in decreasing relative abundance from left to right. The grayscale bar on top shows the estimated relative abundance of CD8+ T-cells in each class of samples – black indicates 100% relative abundance of CD8+ T-cells, white indicates 0% relative abundance of CD8+ T-cells, and grey indicates intermediate relative abundance of CD8+ T-cells. Gene expression values are centered across all samples to a median of zero. All genes mentioned in the text are listed and their position is marked with a black bar.
Figure 4 CD8+ T-cell signature genes. Relative expression of CD8+ T-cell signature genes is shown for all samples. Genes (rows) are sorted in descending order of correlation of gene expression with relative abundance of T-cells. Samples (columns) are ordered in decreasing relative abundance from left to right. The grayscale bar on top shows the estimated relative abundance of CD8+ T-cells in each class of samples – black indicates 100% relative abundance of CD8+ T-cells, white indicates 0% relative abundance of CD8+ T-cells, and grey indicates intermediate relative abundance of CD8+ T-cells. Gene expression values are centered across all samples to a median of zero. All genes mentioned in the text are listed and their position is marked with a black bar.CC BY · PubMed Central
Figure 5 Granulocyte signature genes. Relative expression of granulocyte signature genes is shown for all samples. Genes (rows) are sorted in descending order of correlation of gene expression with relative abundance of granulocytes. Samples (columns) are ordered in decreasing relative abundance from left to right. The grayscale bar on top shows the estimated relative abundance of granulocytes in each class of samples – black indicates 100% relative abundance of granulocytes, white indicates 0% relative abundance of granulocytes, and grey indicates intermediate relative abundance of granulocytes. Gene expression values are centered across all samples to a median of zero. All genes mentioned in the text are listed in order of correlation with granulocyte abundance, and black bars indicate their positions in the figure.
Figure 5 Granulocyte signature genes. Relative expression of granulocyte signature genes is shown for all samples. Genes (rows) are sorted in descending order of correlation of gene expression with relative abundance of granulocytes. Samples (columns) are ordered in decreasing relative abundance from left to right. The grayscale bar on top shows the estimated relative abundance of granulocytes in each class of samples – black indicates 100% relative abundance of granulocytes, white indicates 0% relative abundance of granulocytes, and grey indicates intermediate relative abundance of granulocytes. Gene expression values are centered across all samples to a median of zero. All genes mentioned in the text are listed in order of correlation with granulocyte abundance, and black bars indicate their positions in the figure.CC BY · PubMed Central
Figure 6 Lymphocyte signature genes. Relative expression of lymphocyte signature genes is shown for all samples. Genes (rows) are sorted in ascending order of descending correlation of gene expression with relative abundance of lymphocytes. Samples (columns) are ordered in increasing relative abundance from left to right. The grayscale bar on top shows the estimated relative abundance of lymphocytes in each class of samples – black indicates 100% relative abundance of lymphocytes, white indicates 0% relative abundance of lymphocytes, and grey indicates intermediate relative abundance of lymphocytes. Gene expression values are centered across all samples to a median of zero. All genes mentioned in the text are listed and their position is marked with a black bar.
Figure 6 Lymphocyte signature genes. Relative expression of lymphocyte signature genes is shown for all samples. Genes (rows) are sorted in ascending order of descending correlation of gene expression with relative abundance of lymphocytes. Samples (columns) are ordered in increasing relative abundance from left to right. The grayscale bar on top shows the estimated relative abundance of lymphocytes in each class of samples – black indicates 100% relative abundance of lymphocytes, white indicates 0% relative abundance of lymphocytes, and grey indicates intermediate relative abundance of lymphocytes. Gene expression values are centered across all samples to a median of zero. All genes mentioned in the text are listed and their position is marked with a black bar.CC BY · PubMed Central

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  1. Kuby J: Immunology. 1997, W. H. Freeman and Company, 3

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Metadata

Authors
Palmer, C., Diehn, M., Alizadeh, A. A., & Brown, P. O.
Affiliations
  • Stanford Medicine (US)
  • Howard Hughes Medical Institute (US)
Corresponding author
Brown, Patrick O
ORCID
Venue
BMC Genomics
Publisher
Springer Science and Business Media LLC
Published
2006-05-16
Volume
7
Issue
1
Pages
115-115
ISSN
1471-2164 (ISSN-L)
DOI
10.1186/1471-2164-7-115
PMC
PMC1479811
OpenAlex
W2116830437
Cited by
331
References
43
Citations by year
2026: 8 · 2025: 7 · 2024: 13 · 2023: 12 · 2022: 15 · 2021: 27 · 2020: 26 · 2019: 31 · 2018: 23 · 2017: 31 · 2016: 12 · 2015: 16 · 2014: 18 · 2013: 17 · 2012: 15
FWCI
3.26
Type
journal article
Language
en
Open access
Licence
Locations
  • BMC Genomics (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
Funders
  • Howard Hughes Medical Institute
  • National Institute of General Medical Sciences (T32GM007365, GM 07365)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene expression and cancer classification
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
  • Life Sciences › Immunology and Microbiology › Immunology › T-cell and B-cell Immunology
Keywords
cell type-specific gene expression, leukocytes, B cells, CD4+ T cells, CD8+ T cells, granulocytes, lymphocytes, gene expression signatures, cell surface proteins, ribosomal proteins, inflammatory proteins, peripheral blood
MeSH terms
Adult, B-Lymphocytes, Blood Cells, Cell Separation, Female, Genes, Granulocytes, Humans, Leukocytes, Male, Middle Aged, Organ Specificity, CD4-Positive T-Lymphocytes, T-Lymphocyte Subsets, CD8-Positive T-Lymphocytes, Oligonucleotide Array Sequence Analysis, Gene Expression Profiling

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