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Olsen C, Fleming K, Prendergast N, et al. Using shRNA experiments to validate gene regulatory networks. Genom Data. 2015;4:123-6doi: 10.1016/j.gdata.2015.03.011.
Olsen, C., Fleming, K., Prendergast, N., Rubio, R., Emmert-Streib, F., Bontempi, G., Quackenbush, J., & Haibe-Kains, B. (2015). Using shRNA experiments to validate gene regulatory networks. Genomics data, 4123-6. https://doi.org/10.1016/j.gdata.2015.03.011
Olsen, Catharina, et al. "Using shRNA experiments to validate gene regulatory networks." Genomics data vol. 4 (2015): 123-6. doi: https://doi.org/10.1016/j.gdata.2015.03.011
Olsen C, Fleming K, Prendergast N, Rubio R, Emmert-Streib F, Bontempi G, Quackenbush J, Haibe-Kains B. Using shRNA experiments to validate gene regulatory networks. Genom Data. 2015 Apr 01;4:123-6. doi: 10.1016/j.gdata.2015.03.011. eCollection 2015 Jun. PMID: 26484195; PMCID: PMC4535466.
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Genom Data. 2015 Apr 01;4:123-6. doi: 10.1016/j.gdata.2015.03.011. eCollection 2015 Jun.

Using shRNA experiments to validate gene regulatory networks.

Genomics data

Catharina Olsen, Kathleen Fleming, Niall Prendergast, Renee Rubio, Frank Emmert-Streib, Gianluca Bontempi, John Quackenbush, Benjamin Haibe-Kains

Affiliations

  1. Machine Learning Group, Université Libre de Bruxelles, Brussels, Belgium ; Interuniversity Institute of Bioinformatics in Brussels (IB) , Belgium.
  2. Computational Biology and Functional Genomics Laboratory, Dana-Farber Cancer Institute, Harvard School of Public Health, Boston, MA, USA.
  3. Computational Medicine and Statistical Learning Laboratory, Department of Signal Processing, Tampere University of Technology, Korkeakoulunkatu 1, 33720 Tampere, Finland ; Institute of Biosciences and Medical Technology, Biokatu 10, 33520 Tampere, Finland.
  4. Bioinformatics and Computational Genomics Laboratory, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada ; Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.

PMID: 26484195 PMCID: PMC4535466 DOI: 10.1016/j.gdata.2015.03.011

Abstract

Quantitative validation of gene regulatory networks (GRNs) inferred from observational expression data is a difficult task usually involving time intensive and costly laboratory experiments. We were able to show that gene knock-down experiments can be used to quantitatively assess the quality of large-scale GRNs via a purely data-driven approach (Olsen et al. 2014). Our new validation framework also enables the statistical comparison of multiple network inference techniques, which was a long-standing challenge in the field. In this Data in Brief we detail the contents and quality controls for the gene expression data (available from NCBI Gene Expression Omnibus repository with accession number GSE53091) associated with our study published in Genomics (Olsen et al. 2014). We also provide R code to access the data and reproduce the analysis presented in this article.

Keywords: Colon cancer; Gene expression; Knock-down; Microarray; shRNA

References

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  3. Cancer Res. 1976 Dec;36(12):4562-9 - PubMed
  4. World J Gastrointest Oncol. 2013 May 15;5(5):97-101 - PubMed
  5. Nucleic Acids Res. 2005 Jan 1;33(Database issue):D562-6 - PubMed

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