Literature DB >> 20940121

Bagged gene shaving for the robust clustering of high-throughput data.

Bradley M Broom1, Erik P Sulman, Kim-Anh Do, Mary E Edgerton.   

Abstract

The analysis of high-throughput data sets, such as microarray data, often requires that individual variables (genes, for example) be grouped into clusters of variables with highly correlated values across all samples. Gene shaving is an established method for generating such clusters, but is overly sensitive to the input data: changing just one sample can determine whether or not an entire cluster is found. This paper describes a clustering method based on the bootstrap aggregation of gene shaving clusters, which overcomes this and other problems, and applies the new method to a large gene expression microarray dataset from brain tumour samples.

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Year:  2010        PMID: 20940121      PMCID: PMC3879957          DOI: 10.1504/IJBRA.2010.035997

Source DB:  PubMed          Journal:  Int J Bioinform Res Appl        ISSN: 1744-5485


  4 in total

1.  'Gene shaving' as a method for identifying distinct sets of genes with similar expression patterns.

Authors:  T Hastie; R Tibshirani; M B Eisen; A Alizadeh; R Levy; L Staudt; W C Chan; D Botstein; P Brown
Journal:  Genome Biol       Date:  2000-08-04       Impact factor: 13.583

2.  Loss of heterozygosity on chromosome 10 is more extensive in primary (de novo) than in secondary glioblastomas.

Authors:  H Fujisawa; R M Reis; M Nakamura; S Colella; Y Yonekawa; P Kleihues; H Ohgaki
Journal:  Lab Invest       Date:  2000-01       Impact factor: 5.662

3.  Run batch effects potentially compromise the usefulness of genomic signatures for ovarian cancer.

Authors:  Keith A Baggerly; Kevin R Coombes; E Shannon Neeley
Journal:  J Clin Oncol       Date:  2008-03-01       Impact factor: 44.544

4.  Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data.

Authors:  Manhong Dai; Pinglang Wang; Andrew D Boyd; Georgi Kostov; Brian Athey; Edward G Jones; William E Bunney; Richard M Myers; Terry P Speed; Huda Akil; Stanley J Watson; Fan Meng
Journal:  Nucleic Acids Res       Date:  2005-11-10       Impact factor: 16.971

  4 in total
  3 in total

1.  Bayesian ensemble methods for survival prediction in gene expression data.

Authors:  Vinicius Bonato; Veerabhadran Baladandayuthapani; Bradley M Broom; Erik P Sulman; Kenneth D Aldape; Kim-Anh Do
Journal:  Bioinformatics       Date:  2010-12-08       Impact factor: 6.937

2.  Modulating microtubule stability enhances the cytotoxic response of cancer cells to Paclitaxel.

Authors:  Ahmed Ashour Ahmed; Xiaoyan Wang; Zhen Lu; Juliet Goldsmith; Xiao-Feng Le; Geoffrey Grandjean; Geoffrey Bartholomeusz; Bradley Broom; Robert C Bast
Journal:  Cancer Res       Date:  2011-07-20       Impact factor: 12.701

3.  Model averaging strategies for structure learning in Bayesian networks with limited data.

Authors:  Bradley M Broom; Kim-Anh Do; Devika Subramanian
Journal:  BMC Bioinformatics       Date:  2012-08-24       Impact factor: 3.169

  3 in total

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