RankProd: a bioconductor package for detecting differentially expressed genes in meta-analysis

By Fangxin Hong, Rainer Breitling, Connor W. McEntee, Ben S. Wittner, Jennifer L. Nemhauser, Joanne Chory. Bioinform., 2006

752 citations recorded by the source corpus.

Subfields: Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/2810851502a43c5b4fb960778a50ccafd5a30fc3

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Citations in the corpus

Resveratrol delays age-related deterioration and mimics transcriptional aspects of dietary restriction without extending lifespan (2008, positive): “, 2003), and false discovery rates were estimated using Rankprod (Hong et al., 2006).”
The Arabidopsis NFYA5 Transcription Factor Is Regulated Transcriptionally and Posttranscriptionally to Promote Drought Resistance[W] (2008, methodology): “05) (Gentleman et al., 2004; Hong et al., 2006).”
Rapid synthesis of auxin via a new tryptophan-dependent pathway is required for shade avoidance in plants. (2008, positive): “Comparisons of genotypes and treatments were performed using the RankProd package from Bioconductor (Hong et al., 2006).”
A re‐evaluation of fixed effect(s) meta‐analysis (2018, background): “In some relatively simple setting where only statistical tests are required, all of these small sample issues can be addressed by permutation methods; see for example Hong et al. (2006).”
Key Issues in Conducting a Meta-Analysis of Gene Expression Microarray Datasets (2008, methodology): “Meta-analysis could be used to identify genes expressed differentially between two groups [19,22,29,3 0,32,33,35,37,38,40], to robustify cross-platform classification [34], to identify overlaps between samples from heterologous datasets [30], to identify co-expressed genes, or to reconstruct gene…”
Comprehensive literature review and statistical considerations for microarray meta-analysis (2012, background): “(102) proposed a more advanced RankProd algorithm that calculates the product of the ranks of fold change in each inter-group pair of samples.”
Subtle variations in Pten dose determine cancer susceptibility (2010, methodology): “Genes passing the quality control filter were ranked by signal-to-noise ratio according to their differential expression using the Bioconductor RankProd packag”