Lineage specificity of gene expression patterns.

@article{citeulike:423618, 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.}, address = {Department of Cell Biology, New York University School of Medicine, New York, NY 10016, USA.}, author = {Kluger, Y. and Tuck, D. P. and Chang, J. T. and Nakayama, Y. and Poddar, R. and Kohya, N. and Lian, Z. and Ben Nasr, A. and Halaban, H. R. and Krause, D. S. and Zhang, X. and Newburger, P. E. and Weissman, S. M. }, citeulike-article-id = {423618}, doi = {http://dx.doi.org/10.1073/pnas.0401136101}, issn = {0027-8424}, journal = {Proc Natl Acad Sci U S A}, month = {April}, number = {17}, pages = {6508--6513}, posted-at = {2005-12-06 20:39:18}, priority = {5}, title = {Lineage specificity of gene expression patterns.}, url = {http://dx.doi.org/10.1073/pnas.0401136101}, volume = {101}, year = {2004} }

TY - JOUR ID - citeulike:423618 L3 - citeulike-article-id:423618 TI - Lineage specificity of gene expression patterns. JF - Proc Natl Acad Sci U S A VL - 101 IS - 17 SP - 6508 EP - 6513 AD - Department of Cell Biology, New York University School of Medicine, New York, NY 10016, USA. SN - 0027-8424 N2 - 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. AU - Kluger, Y AU - Tuck, DP AU - Chang, JT AU - Nakayama, Y AU - Poddar, R AU - Kohya, N AU - Lian, Z AU - Ben Nasr, A AU - Halaban, HR AU - Krause, DS AU - Zhang, X AU - Newburger, PE AU - Weissman, SM PY - 2004/04/27/ UR - http://dx.doi.org/10.1073/pnas.0401136101 ER -