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Using shRNA experiments to validate gene regulatory networks

Research output: Contribution to journalArticleScientificpeer-review

Details

Original languageEnglish
Pages (from-to)123-126
Number of pages4
JournalGenomics Data
Volume4
DOIs
Publication statusPublished - 1 Jun 2015
Publication typeA1 Journal article-refereed

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

Publication forum classification

Field of science, Statistics Finland