Identifying periodically expressed transcripts in microarray time series data
By Sofia Wichert, Konstantinos Fokianos, Korbinian Strimmer. Bioinform., 2008
346 citations recorded by the source corpus.
Subfields: Molecular Biology
View Paper: https://www.semanticscholar.org/paper/d0183bd780fd8bc14a3c519ffcbdfb24a04c7a7d
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In Molecular Biology
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Citations in the corpus
- JTK_CYCLE: an efficient non-parametric algorithm for detecting rhythmic components in genome-scale datasets (2010, methodology): “, 2002), curvefitting (Straume, 2004), and Fourier analysis (Wichert et al., 2004).”
- Permutation test for periodicity in short time series data (2006, neutral): “The significance of the observed periodicity can be estimated by Fisher g-statistics, as recently recommended in [11].”
- Sugars and Circadian Regulation Make Major Contributions to the Global Regulation of Diurnal Gene Expression in Arabidopsis[W][OA] (2005, methodology): “This may be an underestimate because GeneTS will not recognize nonsinusoidal changes and noise will mask small changes.”
- Some Results on the Control of the False Discovery Rate under Dependence (2007, methodology): “DNA time-course data are usually treated with a modelling approach, as in Storey et al. (2004a) or Wichert et al. (2004).”
- STEM: a tool for the analysis of short time series gene expression data (2006, background): “For instance, detecting differentially expressed genes in time series data is available in Significance Analysis of Microarrays (SAM) [21] and Extraction of Differential Gene Expression (EDGE) [22], and detecting periodically expressed genes is a function in the GeneTS script [23].”
- Automated genome annotation and pathway identification using the KEGG Orthology (KO) as a controlled vocabulary (2005, methodology): “of sequences. It calculates the FDR value by invoking the GeneTS (2.3) ( Wichert et al., 2004 ) package of the R”
- Analyzing time series gene expression data (2004, methodology): “In addition to the Shedden and Cooper method discussed above, Wichert et al. (2004) used a periodgram, which is also based on Fourier analysis to identify significant peaks in time series expression data.”
- Harmonics of Circadian Gene Transcription in Mammals (2009, methodology): “The second algorithm, Fisher’s G-test [26], uses Fourier transforms to systematically screen experimental data for sinusoidal components.”