Journal: PLoS Computational Biology

Article Title: Computational Predictions Provide Insights into the Biology of TAL Effector Target Sites

doi: 10.1371/journal.pcbi.1002962

Figure Lengend Snippet: We consider as performance measures the number of predicted targets consistent with up-regulation in gene expression microarrays for different rank cutoffs and thresholds of 1 and 0.5 on the log-fold changes (left panel), and the precision-recall (PR) curve (right panel) using a threshold of 1 on the log-fold changes.

Article Snippet: The expression levels of A. thaliana genes are measured by Affymetrix Ath1 microarrays (imaGenes GmbH, Berlin, Germany), RMA normalized, and fold changes are determined for each of the 3 transgenic lines compared to 3 non-transgenic lines independently.

Techniques: Expressing

Journal: PLoS ONE

Article Title: GENE-Counter: A Computational Pipeline for the Analysis of RNA-Seq Data for Gene Expression Differences

doi: 10.1371/journal.pone.0025279

Figure Lengend Snippet: ( A ) Comparison of estimated log 2 -fold changes from analysis of microarrays (x-axis) and RNA-Seq using GENE-counter running NBPSeq (y-axis). Only induced genes measurable by both platforms are presented. Differentially induced genes are colored to highlight genes uniquely identified using microarrays (open red down triangles) or RNA-Seq (open blue up triangles) and found common between the two methods (purple crosses). ( B ) Three-way Venn comparing differentially expressed genes identified from GENE-counter's assessment of RNA-Seq data and analysis of microarrays. Only genes measurable using both methods were included in the comparison.

Article Snippet: The mRNA labeling, hybridization, and scanning of Affymetrix ATH1 microarrays were done by the CGRB core facility at OSU.

Techniques: Comparison, RNA Sequencing