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Using shRNA experiments to validate gene regulatory networks

TitleUsing shRNA experiments to validate gene regulatory networks
Publication TypeJournal Article
Year of Publication2015
AuthorsOlsen, C, Fleming, K, Prendergast, N, Rubio, R, Emmert-Streib, F, Bontempi, G, Quackenbush, J, Haibe-Kains, B
JournalGenomics Data

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.


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