Literature DB >> 16731696

ACE-it: a tool for genome-wide integration of gene dosage and RNA expression data.

Wessel N van Wieringen1, Jeroen A M Belien, Sjoerd J Vosse, Eskeatnaf M Achame, Bauke Ylstra.   

Abstract

SUMMARY: We describe a tool, called ACE-it (Array CGH Expression integration tool). ACE-it links the chromosomal position of the gene dosage measured by array CGH to the genes measured by the expression array. ACE-it uses this link to statistically test whether gene dosage affects RNA expression. AVAILABILITY: ACE-it is freely available at http://ibivu.cs.vu.nl/programs/acewww/.

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Year:  2006        PMID： 16731696     DOI： 10.1093/bioinformatics/btl269

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  17 in total

1.  Lessons from a decade of integrating cancer copy number alterations with gene expression profiles.

Authors:  Norman Huang; Parantu K Shah; Cheng Li
Journal:  Brief Bioinform       Date:  2011-09-23       Impact factor: 11.622

2.  Integrated analysis of DNA copy number and gene expression microarray data using gene sets.

Authors:  Renée X Menezes; Marten Boetzer; Melle Sieswerda; Gert-Jan B van Ommen; Judith M Boer
Journal:  BMC Bioinformatics       Date:  2009-06-29       Impact factor: 3.169

3.  Integrated genomic and transcriptional profiling identifies chromosomal loci with altered gene expression in cervical cancer.

Authors:  Saskia M Wilting; Jillian de Wilde; Chris J L M Meijer; Johannes Berkhof; Yajun Yi; Wessel N van Wieringen; Boudewijn J M Braakhuis; Gerrit A Meijer; Bauke Ylstra; Peter J F Snijders; Renske D M Steenbergen
Journal:  Genes Chromosomes Cancer       Date:  2008-10       Impact factor: 5.006

4.  Matching of array CGH and gene expression microarray features for the purpose of integrative genomic analyses.

Authors:  Wessel N van Wieringen; Kristian Unger; Gwenaël G R Leday; Oscar Krijgsman; Renée X de Menezes; Bauke Ylstra; Mark A van de Wiel
Journal:  BMC Bioinformatics       Date:  2012-05-04       Impact factor: 3.169

Review 5.  Cancer gene prioritization by integrative analysis of mRNA expression and DNA copy number data: a comparative review.

Authors:  Leo Lahti; Martin Schäfer; Hans-Ulrich Klein; Silvio Bicciato; Martin Dugas
Journal:  Brief Bioinform       Date:  2012-03-22       Impact factor: 11.622

Review 6.  A survey of analysis software for array-comparative genomic hybridisation studies to detect copy number variation.

Authors:  Anis Karimpour-Fard; Laura Dumas; Tzulip Phang; James M Sikela; Lawrence E Hunter
Journal:  Hum Genomics       Date:  2010-08       Impact factor: 4.639

7.  CGHregions: dimension reduction for array CGH data with minimal information loss.

Authors:  Mark A van de Wiel; Wessel N van Wieringen
Journal:  Cancer Inform       Date:  2007-02-08

8.  CHESS (CgHExpreSS): a comprehensive analysis tool for the analysis of genomic alterations and their effects on the expression profile of the genome.

Authors:  Mikyung Lee; Yangseok Kim
Journal:  BMC Bioinformatics       Date:  2009-12-16       Impact factor: 3.169

9.  Testing the utility of an integrated analysis of copy number and transcriptomics datasets for inferring gene regulatory relationships.

Authors:  Xin Yi Goh; Richard Newton; Lorenz Wernisch; Rebecca Fitzgerald
Journal:  PLoS One       Date:  2013-05-30       Impact factor: 3.240

10.  SIGMA2: a system for the integrative genomic multi-dimensional analysis of cancer genomes, epigenomes, and transcriptomes.

Authors:  Raj Chari; Bradley P Coe; Craig Wedseltoft; Marie Benetti; Ian M Wilson; Emily A Vucic; Calum MacAulay; Raymond T Ng; Wan L Lam
Journal:  BMC Bioinformatics       Date:  2008-10-07       Impact factor: 3.169
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