Literature DB >> 18097463

The properties of high-dimensional data spaces: implications for exploring gene and protein expression data.

Robert Clarke1, Habtom W Ressom, Antai Wang, Jianhua Xuan, Minetta C Liu, Edmund A Gehan, Yue Wang.   

Abstract

High-throughput genomic and proteomic technologies are widely used in cancer research to build better predictive models of diagnosis, prognosis and therapy, to identify and characterize key signalling networks and to find new targets for drug development. These technologies present investigators with the task of extracting meaningful statistical and biological information from high-dimensional data spaces, wherein each sample is defined by hundreds or thousands of measurements, usually concurrently obtained. The properties of high dimensionality are often poorly understood or overlooked in data modelling and analysis. From the perspective of translational science, this Review discusses the properties of high-dimensional data spaces that arise in genomic and proteomic studies and the challenges they can pose for data analysis and interpretation.

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Year:  2008        PMID: 18097463      PMCID: PMC2238676          DOI: 10.1038/nrc2294

Source DB:  PubMed          Journal:  Nat Rev Cancer        ISSN: 1474-175X            Impact factor:   60.716


  89 in total

1.  Emergence of scaling in random networks

Authors: 
Journal:  Science       Date:  1999-10-15       Impact factor: 47.728

2.  Genome-wide location and function of DNA binding proteins.

Authors:  B Ren; F Robert; J J Wyrick; O Aparicio; E G Jennings; I Simon; J Zeitlinger; J Schreiber; N Hannett; E Kanin; T L Volkert; C J Wilson; S P Bell; R A Young
Journal:  Science       Date:  2000-12-22       Impact factor: 47.728

Review 3.  From patterns to pathways: gene expression data analysis comes of age.

Authors:  Donna K Slonim
Journal:  Nat Genet       Date:  2002-12       Impact factor: 38.330

Review 4.  Hormonal aspects of breast cancer. Growth factors, drugs and stromal interactions.

Authors:  R Clarke; R B Dickson; M E Lippman
Journal:  Crit Rev Oncol Hematol       Date:  1992-01       Impact factor: 6.312

Review 5.  Genome-wide association studies for common diseases and complex traits.

Authors:  Joel N Hirschhorn; Mark J Daly
Journal:  Nat Rev Genet       Date:  2005-02       Impact factor: 53.242

6.  Gene selection for microarray data analysis using principal component analysis.

Authors:  Antai Wang; Edmund A Gehan
Journal:  Stat Med       Date:  2005-07-15       Impact factor: 2.373

Review 7.  Microarray data analysis: from disarray to consolidation and consensus.

Authors:  David B Allison; Xiangqin Cui; Grier P Page; Mahyar Sabripour
Journal:  Nat Rev Genet       Date:  2006-01       Impact factor: 53.242

8.  Genome-wide analysis of estrogen receptor binding sites.

Authors:  Jason S Carroll; Clifford A Meyer; Jun Song; Wei Li; Timothy R Geistlinger; Jérôme Eeckhoute; Alexander S Brodsky; Erika Krasnickas Keeton; Kirsten C Fertuck; Giles F Hall; Qianben Wang; Stefan Bekiranov; Victor Sementchenko; Edward A Fox; Pamela A Silver; Thomas R Gingeras; X Shirley Liu; Myles Brown
Journal:  Nat Genet       Date:  2006-10-01       Impact factor: 38.330

9.  Cluster analysis and display of genome-wide expression patterns.

Authors:  M B Eisen; P T Spellman; P O Brown; D Botstein
Journal:  Proc Natl Acad Sci U S A       Date:  1998-12-08       Impact factor: 11.205

10.  The effects of normalization on the correlation structure of microarray data.

Authors:  Xing Qiu; Andrew I Brooks; Lev Klebanov; Ndrei Yakovlev
Journal:  BMC Bioinformatics       Date:  2005-05-16       Impact factor: 3.169

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  170 in total

1.  PUGSVM: a caBIG™ analytical tool for multiclass gene selection and predictive classification.

Authors:  Guoqiang Yu; Huai Li; Sook Ha; Ie-Ming Shih; Robert Clarke; Eric P Hoffman; Subha Madhavan; Jianhua Xuan; Yue Wang
Journal:  Bioinformatics       Date:  2010-12-24       Impact factor: 6.937

2.  Gene set enrichment; a problem of pathways.

Authors:  Matthew N Davies; Emma L Meaburn; Leonard C Schalkwyk
Journal:  Brief Funct Genomics       Date:  2010-09-22       Impact factor: 4.241

3.  Computational Analysis of Muscular Dystrophy Sub-types Using A Novel Integrative Scheme.

Authors:  Chen Wang; Sook Ha; Jianhua Xuan; Yue Wang; Eric Hoffman
Journal:  Neurocomputing       Date:  2012-09-01       Impact factor: 5.719

Review 4.  Systems biology: perspectives on multiscale modeling in research on endocrine-related cancers.

Authors:  Robert Clarke; John J Tyson; Ming Tan; William T Baumann; Lu Jin; Jianhua Xuan; Yue Wang
Journal:  Endocr Relat Cancer       Date:  2019-06       Impact factor: 5.678

5.  Multivariate statistical identification of human bladder carcinomas using ambient ionization imaging mass spectrometry.

Authors:  Allison L Dill; Livia S Eberlin; Anthony B Costa; Cheng Zheng; Demian R Ifa; Liang Cheng; Timothy A Masterson; Michael O Koch; Olga Vitek; R Graham Cooks
Journal:  Chemistry       Date:  2011-01-31       Impact factor: 5.236

6.  BACOM: in silico detection of genomic deletion types and correction of normal cell contamination in copy number data.

Authors:  Guoqiang Yu; Bai Zhang; G Steven Bova; Jianfeng Xu; Ie-Ming Shih; Yue Wang
Journal:  Bioinformatics       Date:  2011-04-15       Impact factor: 6.937

7.  Antiestrogen Resistance and the Application of Systems Biology.

Authors:  Kerrie B Bouker; Yue Wang; Jianhua Xuan; Robert Clarke
Journal:  Drug Discov Today Dis Mech       Date:  2012-12-01

Review 8.  Analysis of omics data with genome-scale models of metabolism.

Authors:  Daniel R Hyduke; Nathan E Lewis; Bernhard Ø Palsson
Journal:  Mol Biosyst       Date:  2012-12-18

9.  Gene network signaling in hormone responsiveness modifies apoptosis and autophagy in breast cancer cells.

Authors:  Robert Clarke; Ayesha N Shajahan; Rebecca B Riggins; Younsook Cho; Anatasha Crawford; Jianhua Xuan; Yue Wang; Alan Zwart; Ruchi Nehra; Minetta C Liu
Journal:  J Steroid Biochem Mol Biol       Date:  2009-03       Impact factor: 4.292

10.  Cell Painting, a high-content image-based assay for morphological profiling using multiplexed fluorescent dyes.

Authors:  Mark-Anthony Bray; Shantanu Singh; Han Han; Chadwick T Davis; Blake Borgeson; Cathy Hartland; Maria Kost-Alimova; Sigrun M Gustafsdottir; Christopher C Gibson; Anne E Carpenter
Journal:  Nat Protoc       Date:  2016-08-25       Impact factor: 13.491

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