University of California, Berkeley, CA (United States); Max Planck Institute of Molecular Cell Biology and Genetics, Dresdenn (Germany); DOE/OSTI
University of California, Berkeley, CA (United States); University of California, Los Angeles, CA (United States)
University of California, Berkeley, CA (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
University of California, Berkeley, CA (United States); Howard Hughes Medical Institute, Berkeley, CA (United States)
University of California, Los Angeles, CA (United States)
University of California, Berkeley, CA (United States); Howard Hughes Medical Institute, Berkeley, CA (United States); Janelia Farm Research Campus, Ashburn, VA (United States)
Cell and tissue specific gene expression is a defining feature of embryonic development in multi-cellular organisms. However, the range of gene expression patterns, the extent of the correlation of expression with function, and the classes of genes whose spatial expression are tightly regulated have been unclear due to the lack of an unbiased, genome-wide survey of gene expression patterns. We determined and documented embryonic expression patterns for 6,003 (44%) of the 13,659 protein-coding genes identified in the Drosophila melanogaster genome with over 70,000 images and controlled vocabulary annotations. Individual expression patterns are extraordinarily diverse, but by supplementing qualitative in situ hybridization data with quantitative microarray time-course data using a hybrid clustering strategy, we identify groups of genes with similar expression. Of 4,496 genes with detectable expression in the embryo, 2,549 (57%) fall into 10 clusters representing broad expression patterns. The remaining 1,947 (43%) genes fall into 29 clusters representing restricted expression, 20% patterned as early as blastoderm, with the majority restricted to differentiated cell types, such as epithelia, nervous system, or muscle. We investigate the relationship between expression clusters and known molecular and cellular physiological functions. Nearly 60% of the genes with detectable expression exhibit broad patterns reflecting quantitative rather than qualitative differences between tissues. The other 40% show tissue restricted expression; the expression patterns of over 1,500 of these genes are documented here for the first time. Within each of these categories, we identified clusters of genes associated with particular cellular and developmental functions.
Tomancak, Pavel, Berman, Benjamin P., Beaton, Amy, Weiszmann, Richard, Kwan, Elaine, Hartenstein, Volker, Celniker, Susan E., & Rubin, Gerald M. (2007). <strong>Global analysis of patterns of gene expression during <em>Drosophila</em>embryogenesis</strong>. GenomeBiology.com, 8(7). https://doi.org/10.1186/gb-2007-8-7-r145
Tomancak, Pavel, Berman, Benjamin P., Beaton, Amy, et al., "<strong>Global analysis of patterns of gene expression during <em>Drosophila</em>embryogenesis</strong>," GenomeBiology.com 8, no. 7 (2007), https://doi.org/10.1186/gb-2007-8-7-r145
@article{osti_1626720,
author = {Tomancak, Pavel and Berman, Benjamin P. and Beaton, Amy and Weiszmann, Richard and Kwan, Elaine and Hartenstein, Volker and Celniker, Susan E. and Rubin, Gerald M.},
title = {<strong>Global analysis of patterns of gene expression during <em>Drosophila</em>embryogenesis</strong>},
annote = {Cell and tissue specific gene expression is a defining feature of embryonic development in multi-cellular organisms. However, the range of gene expression patterns, the extent of the correlation of expression with function, and the classes of genes whose spatial expression are tightly regulated have been unclear due to the lack of an unbiased, genome-wide survey of gene expression patterns. We determined and documented embryonic expression patterns for 6,003 (44%) of the 13,659 protein-coding genes identified in the Drosophila melanogaster genome with over 70,000 images and controlled vocabulary annotations. Individual expression patterns are extraordinarily diverse, but by supplementing qualitative in situ hybridization data with quantitative microarray time-course data using a hybrid clustering strategy, we identify groups of genes with similar expression. Of 4,496 genes with detectable expression in the embryo, 2,549 (57%) fall into 10 clusters representing broad expression patterns. The remaining 1,947 (43%) genes fall into 29 clusters representing restricted expression, 20% patterned as early as blastoderm, with the majority restricted to differentiated cell types, such as epithelia, nervous system, or muscle. We investigate the relationship between expression clusters and known molecular and cellular physiological functions. Nearly 60% of the genes with detectable expression exhibit broad patterns reflecting quantitative rather than qualitative differences between tissues. The other 40% show tissue restricted expression; the expression patterns of over 1,500 of these genes are documented here for the first time. Within each of these categories, we identified clusters of genes associated with particular cellular and developmental functions.},
doi = {10.1186/gb-2007-8-7-r145},
url = {https://www.osti.gov/biblio/1626720},
journal = {GenomeBiology.com},
issn = {ISSN 1465-6906},
number = {7},
volume = {8},
place = {United States},
publisher = {BioMed Central},
year = {2007},
month = {07}}
KDD '15: The 21th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, Proceedings of the 21th ACM SIGKDD International Conference on Knowledge Discovery and Data Mininghttps://doi.org/10.1145/2783258.2783304