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AnnotationDbi, methods, RUnit, annotate, DBI, R(>=2.7.0), AnnotationDbi(>=1.34.3), org.At.tair.db(>=3.3.0)
Integrating roots into a whole plant network of flowering time genes in Arabidopsis thaliana
[…] lower than expected were tested for under-representation (p-value ≤0.01).The Gene Ontology Enrichment analysis was performed using the topGO package V2.20.0 with the annotation of the ATH1 array from ath1121501.db package V3.1.4. We performed a Biological Process (BP) enrichment analysis using the classic Fisher’s exact test (p < 0.001). Redundant GO terms were removed using REVIGO (http://revigo. […]
Discovery of Core Biotic Stress Responsive Genes in Arabidopsis by Weighted Gene Co Expression Network Analysis
[…] Gene Ontology (GO) enrichment in modules was carried out with topGO v. 2.12.0  using the annotation of the ATH1 array from the ath1121501.db R package v. 2.9.0 . The classic Fisher’s exact test method was applied. Each module was tested for enrichment in terms of the Molecular Function (MF) and the Biological Process (BP) c […]
A comparison of the low temperature transcriptomes and CBF regulons of three plant species that differ in freezing tolerance: Solanum commersonii, Solanum tuberosum, and Arabidopsis thaliana
[…] ts function to select probe sets with a ≥2-fold difference between treatment and control with a significance after FDR adjustment of <0.05. Probe sets were mapped to A. thaliana transcripts using the ath1121501.db Bioconductor package (http://www.bioconductor.org/packages/2.5/data/annotation/html/ath1121501.db.html). Transcripts were identified as differentially expressed in each category: early c […]
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