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A global map of human gene expression

Nature Biotechnology volume 28, pages 322–324 (2010)Cite this article

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Although there is only one human genome sequence, different genes are expressed in many different cell types and tissues, as well as in different developmental stages or diseases. The structure of this 'expression space' is still largely unknown, as most transcriptomics experiments focus on sampling small regions. We have constructed a global gene expression map by integrating microarray data from 5,372 human samples representing 369 different cell and tissue types, disease states and cell lines. These have been compiled in an online resource (http://www.ebi.ac.uk/gxa/array/U133A) that allows the user to search for a gene of interest and find the conditions in which it is over- or underexpressed, or, conversely, to find which genes are over- or underexpressed in a particular condition. An analysis of the structure of the expression space reveals that it can be described by a small number of distinct expression profile classes and that the first three principal components of this space have biological interpretations. The hematopoietic system, solid tissues and incompletely differentiated cell types are arranged on the first principal axis; cell lines, neoplastic samples and non-neoplastic primary tissue–derived samples are on the second principal axis; and nervous system is separated from the rest of the samples on the third axis. We also show below that most cell lines cluster together rather than with their tissues of origin.

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Figure 1: Principal component analysis.

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Acknowledgements

We thank P. Adler, J. Bahler, E. Birney, D. Brazma, I. Dunham, N. Gehlenborg, F. Holstege, S. Kaski, M. Krestyaninova, J. Rung, G. Rustici, T. Schlitt and H. Zang-Bradley for helpful comments and discussion. This research was partly funded by FELICS (021902) and EMERALD (LSHG-CT-2006-037689) grants from the European Commission, a MAGE grant from the National Human Genome Research Institute and National Institutes of Biomedical Imaging and Bioengineering from the National Institute of Health (1 P41 HG003619-01), an ALGODAN CoE grant of the Academy of Finland, and grant no. 40274/06 from Finnish Funding agency for Technology and Innovation (TEKES).

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Authors and Affiliations

  1. European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK

    Margus Lukk, Misha Kapushesky, Helen Parkinson, Angela Goncalves, Wolfgang Huber & Alvis Brazma

  2. Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland

    Janne Nikkilä

  3. Department of Computer Science, University of Helsinki, Helsinki, Finland

    Esko Ukkonen

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  1. Margus Lukk
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  2. Misha Kapushesky
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Correspondence to Alvis Brazma.

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Lukk, M., Kapushesky, M., Nikkilä, J. et al. A global map of human gene expression. Nat Biotechnol 28, 322–324 (2010). https://doi.org/10.1038/nbt0410-322

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