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Gene Expression Commons: An Open Platform for Absolute Gene Expression Profiling

Author

Listed:
  • Jun Seita
  • Debashis Sahoo
  • Derrick J Rossi
  • Deepta Bhattacharya
  • Thomas Serwold
  • Matthew A Inlay
  • Lauren I R Ehrlich
  • John W Fathman
  • David L Dill
  • Irving L Weissman

Abstract

Gene expression profiling using microarrays has been limited to comparisons of gene expression between small numbers of samples within individual experiments. However, the unknown and variable sensitivities of each probeset have rendered the absolute expression of any given gene nearly impossible to estimate. We have overcome this limitation by using a very large number (>10,000) of varied microarray data as a common reference, so that statistical attributes of each probeset, such as the dynamic range and threshold between low and high expression, can be reliably discovered through meta-analysis. This strategy is implemented in a web-based platform named “Gene Expression Commons” (https://gexc.stanford.edu/) which contains data of 39 distinct highly purified mouse hematopoietic stem/progenitor/differentiated cell populations covering almost the entire hematopoietic system. Since the Gene Expression Commons is designed as an open platform, investigators can explore the expression level of any gene, search by expression patterns of interest, submit their own microarray data, and design their own working models representing biological relationship among samples.

Suggested Citation

  • Jun Seita & Debashis Sahoo & Derrick J Rossi & Deepta Bhattacharya & Thomas Serwold & Matthew A Inlay & Lauren I R Ehrlich & John W Fathman & David L Dill & Irving L Weissman, 2012. "Gene Expression Commons: An Open Platform for Absolute Gene Expression Profiling," PLOS ONE, Public Library of Science, vol. 7(7), pages 1-11, July.
    • Handle: RePEc:plo:pone00:0040321
    DOI: 10.1371/journal.pone.0040321
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    References listed on IDEAS

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    1. Hong Ji & Lauren I. R. Ehrlich & Jun Seita & Peter Murakami & Akiko Doi & Paul Lindau & Hwajin Lee & Martin J. Aryee & Rafael A. Irizarry & Kitai Kim & Derrick J. Rossi & Matthew A. Inlay & Thomas Ser, 2010. "Comprehensive methylome map of lineage commitment from haematopoietic progenitors," Nature, Nature, vol. 467(7313), pages 338-342, September.
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