Bootstrapping cluster analysis: Assessing the reliability of conclusions from microarray experiments

By M. Kerr, Gary A. Churchill. Proceedings of the National Academy of Sciences of the United States of America, 2001

492 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/f3464c1e3911593ff53bd822e9fed07ae6093695

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Citations in the corpus

Microarray data analysis: from disarray to consolidation and consensus (2006, background): “A consensus has emerged that resampling techniques can assess the reproducibility of unsupervised classification and should be use”
Assessing Gene Significance from cDNA Microarray Expression Data via Mixed Models (2001, unknown): “Our proposed methodology is complementary to various popular clustering methods (refer to Eisen et al ., 1998; Tamayo et al ., 1999; Claverie, 1999; Hastie et al ., 2000; Dudoit et al ., 2001a; Lazzeroni and Owen, 2000; Kerr and Churchill, 2001a).”
From patterns to pathways: gene expression data analysis comes of age (2002, methodology): “Several microarray studies have incorporated these techniques, either using simple but reasonable noise models 35,51 , or by sampling the noise distribution directly from the data 52 .”
MAANOVA: A Software Package for the Analysis of Spotted cDNA Microarray Experiments (2003, methodology): “The MAANOVA software includes features to assess the reliability of C by boot- strapping (Kerr and Churchill 2001c).”
Co-clustering of biological networks and gene expression data (2002, methodology): “This leads to the conclusion that resampling or bootstrapping methods (e.g., Kerr and Churchill (2001)) should be applied to detect the reliable cores of the computed clusters.”
Comparisons and validation of statistical clustering techniques for microarray gene expression data (2003, methodology): “Kerr and Churchill (2001) used a linear model (ANOVA) and residual based resampling to access the reliability of clustering algorithms.”
Network-Based Functional Regions (2011, unknown): “There are a number of studies which utilise `bootstrap resampling' (Elfron and Tibshirani, 1993) to assess the stability of detected clusters, as well as to determine the `true' number of clusters in a dataset (eg, Felsenstein, 1985; Hennig, 2007; Kerr and Churchill, 2001).”
Clustering Stability: An Overview (2010, unknown): “• If we work in a model-based framework, sample data from the model (Kerr and Churchill, 2001).”
Discovering regulatory and signalling circuits in molecular interaction networks (2002, unknown): “, 1999), significance testing (Kerr and Churchill, 2001; Rocke and Durbin, 2001; Ideker et al., 2000), and sequence motif identification (Pilpel et al.”
A high-fat diet coordinately downregulates genes required for mitochondrial oxidative phosphorylation in skeletal muscle. (2005, methodology): “After normalization, gene shaving (22), bootstrapping (23), and cluster analysis were performed (24), and the slide effect, dye effect, variety effect, and duplicate design were taken into account in an ANOVA model (25).”
Cluster Validation by Prediction Strength (2005, methodology): “Kerr and Churchill (2001) used an analysis of variance model to estimate differential expression of genes across multiple conditions and to account for other sources of variation in microarray data.”
Computational cluster validation in post-genomic data analysis (2005, methodology): “Forthispurpose, anumberofbootstrapdatasetsare generated from the original data: using a simple error model (Bittner et al ., 2000) or more advanced methods such as ANOVA (Kerr and Churchill, 2001), a noise component is added to each data item.”
Empirical Bayes Analysis of a Microarray Experiment (2001, background): “The statistics literature for microarrays, still in its infancy and with much of it unpublished, has tended to focus on frequentist data-analytic devices such as cluster analysis, bootstrapping, and linear models (see Li and Wong 2000; Kerr and Churchill 2000; Black and Doerge 2000; Van del Laan and”
Pvclust: an R package for assessing the uncertainty in hierarchical clustering (2006, methodology): “D ow nloaded from https://academ ic.oup.com /bioinform atics/article/22/12/1540/207339 by guest on 03 July 2022 as that of Kerr and Churchill (2001) for DNA microarray analysis, should be incorporated into the program in a future work.”
Is My Network Module Preserved and Reproducible? (2011, unknown): “Our co-clustering statistic (in the first section of Supplementary Text S1) is similar to the cluster robustness measure [23,51] and the accuracy based measures are conceptually related to a cluster discrepancy measure proposed in [23].”