Literature DB >> 18208590

An improved method for detecting and delineating genomic regions with altered gene expression in cancer.

Björn Nilsson1, Mikael Johansson, Anders Heyden, Sven Nelander, Thoas Fioretos.   

Abstract

Genomic regions with altered gene expression are a characteristic feature of cancer cells. We present a novel method for identifying such regions in gene expression maps. This method is based on total variation minimization, a classical signal restoration technique. In systematic evaluations, we show that our method combines top-notch detection performance with an ability to delineate relevant regions without excessive over-segmentation, making it a significant advance over existing methods. Software (Rendersome) is provided.

Entities:  

Mesh：

Year:  2008        PMID： 18208590      PMCID： PMC2395254          DOI： 10.1186/gb-2008-9-1-r13

Source DB:  PubMed          Journal:  Genome Biol        ISSN： 1474-7596            Impact factor:   13.583


  45 in total

1.  Expression imbalance map: a new visualization method for detection of mRNA expression imbalance regions.

Authors:  Makoto Kano; Kunihiro Nishimura; Shumpei Ishikawa; Shuichi Tsutsumi; Koichi Hirota; Michitaka Hirose; Hiroyuki Aburatani
Journal:  Physiol Genomics       Date:  2003-03-18       Impact factor: 3.107

2.  A versatile statistical analysis algorithm to detect genome copy number variation.

Authors:  Raoul-Sam Daruwala; Archisman Rudra; Harry Ostrer; Robert Lucito; Michael Wigler; Bud Mishra
Journal:  Proc Natl Acad Sci U S A       Date:  2004-11-08       Impact factor: 11.205

3.  A molecular classification of papillary renal cell carcinoma.

Authors:  Ximing J Yang; Min-Han Tan; Hyung L Kim; Jonathon A Ditlev; Mark W Betten; Carolina E Png; Eric J Kort; Kunihiko Futami; Kyle A Furge; Masayuki Takahashi; Hiro-Omi Kanayama; Puay Hoon Tan; Bin Sing Teh; Chunyan Luan; Kim Wang; Michael Pins; Maria Tretiakova; John Anema; Richard Kahnoski; Theresa Nicol; Walter Stadler; Nicholas G Vogelzang; Robert Amato; David Seligson; Robert Figlin; Arie Belldegrun; Craig G Rogers; Bin Tean Teh
Journal:  Cancer Res       Date:  2005-07-01       Impact factor: 12.701

4.  Genome scanning with array CGH delineates regional alterations in mouse islet carcinomas.

Authors:  G Hodgson; J H Hager; S Volik; S Hariono; M Wernick; D Moore; N Nowak; D G Albertson; D Pinkel; C Collins; D Hanahan; J W Gray
Journal:  Nat Genet       Date:  2001-12       Impact factor: 38.330

5.  Visualizing chromosomes as transcriptome correlation maps: evidence of chromosomal domains containing co-expressed genes--a study of 130 invasive ductal breast carcinomas.

Authors:  Fabien Reyal; Nicolas Stransky; Isabelle Bernard-Pierrot; Anne Vincent-Salomon; Yann de Rycke; Paul Elvin; Andrew Cassidy; Alexander Graham; Carolyn Spraggon; Yoann Désille; Alain Fourquet; Claude Nos; Pierre Pouillart; Henri Magdelénat; Dominique Stoppa-Lyonnet; Jérôme Couturier; Brigitte Sigal-Zafrani; Bernard Asselain; Xavier Sastre-Garau; Olivier Delattre; Jean Paul Thiery; François Radvanyi
Journal:  Cancer Res       Date:  2005-02-15       Impact factor: 12.701

6.  Regional copy number-independent deregulation of transcription in cancer.

Authors:  Nicolas Stransky; Céline Vallot; Fabien Reyal; Isabelle Bernard-Pierrot; Sixtina Gil Diez de Medina; Rick Segraves; Yann de Rycke; Paul Elvin; Andrew Cassidy; Carolyn Spraggon; Alexander Graham; Jennifer Southgate; Bernard Asselain; Yves Allory; Claude C Abbou; Donna G Albertson; Jean Paul Thiery; Dominique K Chopin; Daniel Pinkel; François Radvanyi
Journal:  Nat Genet       Date:  2006-11-12       Impact factor: 38.330

7.  Combined high-resolution array-based comparative genomic hybridization and expression profiling of ETV6/RUNX1-positive acute lymphoblastic leukemias reveal a high incidence of cryptic Xq duplications and identify several putative target genes within the commonly gained region.

Authors:  H Lilljebjörn; M Heidenblad; B Nilsson; C Lassen; A Horvat; J Heldrup; M Behrendtz; B Johansson; A Andersson; T Fioretos
Journal:  Leukemia       Date:  2007-08-09       Impact factor: 11.528

8.  Genome-wide identification of chromosomal regions of increased tumor expression by transcriptome analysis.

Authors:  Yan Zhou; Shiuh-Ming Luoh; Yan Zhang; Colin Watanabe; Thomas D Wu; Michael Ostland; William I Wood; Zemin Zhang
Journal:  Cancer Res       Date:  2003-09-15       Impact factor: 12.701

9.  Formation of der(19)t(1;19)(q23;p13) in acute lymphoblastic leukemia.

Authors:  Kajsa Paulsson; Andrea Horvat; Thoas Fioretos; Felix Mitelman; Bertil Johansson
Journal:  Genes Chromosomes Cancer       Date:  2005-02       Impact factor: 5.006

10.  Comparison of array-based comparative genomic hybridization with gene expression-based regional expression biases to identify genetic abnormalities in hepatocellular carcinoma.

Authors:  Kyle A Furge; Karl J Dykema; Coral Ho; Xin Chen
Journal:  BMC Genomics       Date:  2005-05-09       Impact factor: 3.969
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  12 in total

1.  Negative regulation of tumor suppressor p53 by microRNA miR-504.

Authors:  Wenwei Hu; Chang S Chan; Rui Wu; Cen Zhang; Yvonne Sun; Jun S Song; Laura H Tang; Arnold J Levine; Zhaohui Feng
Journal:  Mol Cell       Date:  2010-06-11       Impact factor: 17.970

2.  Network modeling of the transcriptional effects of copy number aberrations in glioblastoma.

Authors:  Rebecka Jörnsten; Tobias Abenius; Teresia Kling; Linnéa Schmidt; Erik Johansson; Torbjörn E M Nordling; Bodil Nordlander; Chris Sander; Peter Gennemark; Keiko Funa; Björn Nilsson; Linda Lindahl; Sven Nelander
Journal:  Mol Syst Biol       Date:  2011-04-26       Impact factor: 11.429

3.  Gene set enrichment analysis using linear models and diagnostics.

Authors:  Assaf P Oron; Zhen Jiang; Robert Gentleman
Journal:  Bioinformatics       Date:  2008-09-11       Impact factor: 6.937

4.  A somatic-mutational process recurrently duplicates germline susceptibility loci and tissue-specific super-enhancers in breast cancers.

Authors:  Dominik Glodzik; Sandro Morganella; Helen Davies; Peter T Simpson; Yilong Li; Xueqing Zou; Javier Diez-Perez; Johan Staaf; Ludmil B Alexandrov; Marcel Smid; Arie B Brinkman; Inga Hansine Rye; Hege Russnes; Keiran Raine; Colin A Purdie; Sunil R Lakhani; Alastair M Thompson; Ewan Birney; Hendrik G Stunnenberg; Marc J van de Vijver; John W M Martens; Anne-Lise Børresen-Dale; Andrea L Richardson; Gu Kong; Alain Viari; Douglas Easton; Gerard Evan; Peter J Campbell; Michael R Stratton; Serena Nik-Zainal
Journal:  Nat Genet       Date:  2017-01-23       Impact factor: 38.330

5.  Precise fluorophore lifetime mapping in live-cell, multi-photon excitation microscopy.

Authors:  Ching-Wei Chang; Mary-Ann Mycek
Journal:  Opt Express       Date:  2010-04-12       Impact factor: 3.894

6.  Virtual CGH: an integrative approach to predict genetic abnormalities from gene expression microarray data applied in lymphoma.

Authors:  Huimin Geng; Javeed Iqbal; Wing C Chan; Hesham H Ali
Journal:  BMC Med Genomics       Date:  2011-04-12       Impact factor: 3.063

7.  SegCorr a statistical procedure for the detection of genomic regions of correlated expression.

Authors:  Eleni Ioanna Delatola; Emilie Lebarbier; Tristan Mary-Huard; François Radvanyi; Stéphane Robin; Jennifer Wong
Journal:  BMC Bioinformatics       Date:  2017-07-11       Impact factor: 3.169

8.  Bayesian DNA copy number analysis.

Authors:  Paola M V Rancoita; Marcus Hutter; Francesco Bertoni; Ivo Kwee
Journal:  BMC Bioinformatics       Date:  2009-01-08       Impact factor: 3.169

9.  Recurrent transcriptional clusters in the genome of mouse pluripotent stem cells.

Authors:  Stavroula Skylaki; Simon R Tomlinson
Journal:  Nucleic Acids Res       Date:  2012-07-12       Impact factor: 16.971

10.  Mutational mechanisms of amplifications revealed by analysis of clustered rearrangements in breast cancers.

Authors:  D Głodzik; C Purdie; I H Rye; P T Simpson; J Staaf; P N Span; H G Russnes; S Nik-Zainal
Journal:  Ann Oncol       Date:  2018-11-01       Impact factor: 32.976
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