ArticleProceedings of the National Academy of Sciences of the United States of America2004
Lineage specificity of gene expression patterns.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Unico: a unified model for cell-type resolution genomics from heterogeneous omics data.Genome biology · 2025Article
- The TCF4 Trinucleotide Repeat Expansion of Fuchs' Endothelial Corneal Dystrophy: Implications for the Anterior Segment of the Eye.Investigative ophthalmology & visual science · 2023Article
- Neutrophils in innate immunity and systems biology-level approaches.Wiley interdisciplinary reviews. Systems biology and medicine · 2020Article
- Deblender: a semi-/unsupervised multi-operational computational method for complete deconvolution of expression data from heterogeneous samples.BMC bioinformatics · 2018Article
- Characterizing the replicability of cell types defined by single cell RNA-sequencing data using MetaNeighbor.Nature communications · 2018Article
- Differential gene expression of the intermediate and outer interzone layers of developing articular cartilage in murine embryos.Stem cells and development · 2014Article
- Transcriptomes of the B and T lineages compared by multiplatform microarray profiling.Journal of immunology (Baltimore, Md. : 1950) · 2011Article
- Prediction of the clinical outcome in invasive candidiasis patients based on molecular fingerprints of five anti-Candida antibodies in serum.Molecular & cellular proteomics : MCP · 2011Article
- Directed stem cell differentiation: the role of physical forces.Cell communication & adhesion · 2010Review
- Growth factors, matrices, and forces combine and control stem cells.Science (New York, N.Y.) · 2009Review
- A myelopoiesis-associated regulatory intergenic noncoding RNA transcript within the human HOXA cluster.Blood · 2009Article
- Expression patterns and prognostic value of Bag-1 and Bcl-2 in breast cancer.Breast cancer research : BCR · 2008Article
- Gene expression programs of human smooth muscle cells: tissue-specific differentiation and prognostic significance in breast cancers.PLoS genetics · 2007Article
- Characterizing disease states from topological properties of transcriptional regulatory networks.BMC bioinformatics · 2006Article
- Two types of precursor cells in a multipotential hematopoietic cell line.Proceedings of the National Academy of Sciences of the United States of America · 2005Article
- Memory T cells have gene expression patterns intermediate between naive and effector.Proceedings of the National Academy of Sciences of the United States of America · 2005Article
- Role of neutrophils in innate immunity: a systems biology-level approach.Wiley interdisciplinary reviews. Systems biology and medicineReview
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Authors and funding
13 authors.
Funding
Abstract
The hematopoietic system offers many advantages as a model for understanding general aspects of lineage choice and specification. Using oligonucleotide microarrays, we compared gene expression patterns of multiple purified hematopoietic cell populations, including neutrophils, monocytes, macrophages, resting, centrocytic, and centroblastic B lymphocytes, dendritic cells, and hematopoietic stem cells. Some of these cells were studied under both resting and stimulated conditions. We studied the collective behavior of subsets of genes derived from the Biocarta database of functional pathways, hand-tuned groupings of genes into broad functional categories based on the Gene Ontology database, and the metabolic pathways in the Kyoto Encyclopedia of Genes and Genomes database. Principal component analysis revealed strikingly pervasive differences in relative levels of gene expression among cell lineages that involve most of the subsets examined. These results indicate that many processes in these cells behave differently in different lineages. Much of the variation among lineages was captured by the first few principal components. Principal components biplots were found to provide a convenient visual display of the contributions of the various genes within the subsets in lineage discrimination. Moreover, by applying tree-constructing methodologies borrowed from phylogenetics to the expression data from differentiated cells and stem cells, we reconstructed a tree of relationships that resembled the established hematopoietic program of lineage development. Thus, the mRNA expression data implicitly contained information about developmental relationships among cell types.
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