Cell-type specific gene expression profiles of leukocytes in human peripheral blood
Open accessAbstract
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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Demuxlet is fast, accurate, scalable, and compatible with standard input formats.
“Inspired by models and algorithms developed for detecting contamination in DNA sequencing18, demuxlet is fast, accurate, scalable, and compatible with standard input formats17, 19, 20.”
From Multiplexed droplet single-cell RNA-sequencing using natural genetic variation (2018) · cites this paper as [19]
The Methods sections describe leukocyte gene-expression microarrays and data filtering, not demuxlet. Searches for demuxlet, demultiplexing, scalability, and standard input formats found no passage in our copy addressing the claimed properties. No page numbers were available for these sections. (LLM, conf=0.78)
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- 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
- Venue
- BMC Genomics
- Published
- 2006-05-16
- Volume
- 7
- Issue
- 1
- Pages
- 115-115
- ISSN
- 1471-2164 (ISSN-L)
- 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
- gold
- doi.org
- 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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