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:

Article Title: Transcriptome Analyses Show Changes in Gene Expression to Accompany Pollen Germination and Tube Growth in Arabidopsis 1 [W] [OA]

doi: 10.1104/pp.108.126375

Figure Lengend Snippet: Confirmation of transcriptional profiles of the selected genes by real-time PCR. HP-MP and PT-MP ratios in microarray data of 24 tested genes were compared with the real-time PCR results. The sequences of the gene-specific primers used for PCR are listed in Supplemental Table S8.

Article Snippet: In total, 5,640 genes (representing 25.0% of the unigene targets on the ATH1 microarray) were present in at least one of the three stages (MP, HP, and PT).

Techniques: Real-time Polymerase Chain Reaction, Microarray

Journal:

Article Title: Transcriptome Analyses Show Changes in Gene Expression to Accompany Pollen Germination and Tube Growth in Arabidopsis 1 [W] [OA]

doi: 10.1104/pp.108.126375

Figure Lengend Snippet: Numbers of expressed genes, specifically expressed genes, and transcriptionally changed genes during PG and PTG The first column indicates the three stages (MP, HP, and PT) and two processes (PG and PTG). The “Number of Genes” and “Percentage” columns refer to the numbers of expressed genes, specifically expressed genes, and transcriptionally changed genes as well as the relative percentages.

Article Snippet: In total, 5,640 genes (representing 25.0% of the unigene targets on the ATH1 microarray) were present in at least one of the three stages (MP, HP, and PT).

Techniques:

Journal:

Article Title: Transcriptome Analyses Show Changes in Gene Expression to Accompany Pollen Germination and Tube Growth in Arabidopsis 1 [W] [OA]

doi: 10.1104/pp.108.126375

Figure Lengend Snippet: Numbers of CaM/CML, CHX, and Hsp genes expressed and transcriptionally changed during PG and PTG The first column indicates the name of the gene family. The gene number in the column “Genome” represents the total number for each gene family in the Arabidopsis genome, and the number in the column “ATH1” shows the gene number included in the ATH1 chip for each family. The following three columns show the numbers of expressed genes in three different stages (MP, HP, and PT). The four right columns refer to the numbers of transcriptionally up-regulated (Up) and down-regulated (Down) genes during PG and PTG. For more details, see Supplemental Table S6 and S7.

Article Snippet: In total, 5,640 genes (representing 25.0% of the unigene targets on the ATH1 microarray) were present in at least one of the three stages (MP, HP, and PT).

Techniques:

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