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ESTOOLS Data@Hand: human stem cell gene expression resource

Nature Methods volume 10, pages 814–815 (2013)Cite this article

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To the Editor:

We developed ESTOOLS Data@Hand, a resource to facilitate exploration of published gene expression array data in stem cell research. The resource, updated four times a year, offers efficient sample identification, preprocessing that enables cross-experiment comparisons and computational analysis.

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Figure 1: Gene expression data and analysis workflows in ESTOOLS Data@Hand.

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Acknowledgements

See Supplementary Methods.

Author information

Author notes

  1. Christophe Roos

    Present address: Present address: Euformatics Oy, Espoo, Finland.,

  2. Lingjia Kong, Kaisa-Leena Aho, Kirsi Granberg and Riikka Lund: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Signal Processing, Tampere University of Technology, Tampere, Finland

    Lingjia Kong, Kaisa-Leena Aho, Kirsi Granberg, Laura Järvenpää, Janne Seppälä, Kalle Leinonen, Lauri Hahne, Jarno Mäkelä, Kirsti Laurila, Heidi Pukkila, Olli Yli-Harja, Matti Nykter, Christophe Roos & Reija Autio

  2. Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland

    Lingjia Kong, Riikka Lund, Lauri Hahne, Elisa Närvä, Riitta Lahesmaa & Reija Autio

  3. Centre for Stem Cell Biology and the Department of Biomedical Science, University of Sheffield, Western Bank, Sheffield, UK

    Paul Gokhale & Peter W Andrews

  4. Institute for Systems Biology, Seattle, Washington, USA

    Olli Yli-Harja

Authors
  1. Lingjia Kong
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  18. Christophe Roos
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Corresponding author

Correspondence to Christophe Roos.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Figures, Tables, Notes, and Text

Supplementary Figures 1–8, Supplementary Tables 1, 3, 7, 9 and 10, Supplementary Notes 1 and 2, and Supplementary Methods (PDF 2706 kb)

Supplementary Table 2

Sample sets included in the ESTOOLS Data@Hand resource. (XLSX 13 kb)

Supplementary Table 4

Number of samples by cell and tissue type. (XLSX 10 kb)

Supplementary Table 5

Sample annotations. (XLS 1420 kb)

Supplementary Table 6

The 74 genes expressed greater than 8-fold (adjusted P < 0.001) in hES cells compared to three clusters of differentiated cells. (XLSX 15 kb)

Supplementary Table 8

74 genes coexpressed with LIN28A (including LIN28A) across the Affymetrix sample metadataset (correlation > 0.85, P < 0.001). (XLS 28 kb)

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Kong, L., Aho, KL., Granberg, K. et al. ESTOOLS Data@Hand: human stem cell gene expression resource. Nat Methods 10, 814–815 (2013). https://doi.org/10.1038/nmeth.2576

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