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

Genome Biology
Björn NilssonT 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.

References

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Citations

Sep 16, 2008·Bioinformatics·Assaf P OronRobert Gentleman
Oct 21, 2010·Bioinformatics·Sandro MorganellaMichele Ceccarelli
Jul 17, 2012·Nucleic Acids Research·Stavroula Skylaki, Simon R Tomlinson
Jan 10, 2009·BMC Bioinformatics·Paola M V RancoitaIvo Kwee
Apr 29, 2011·Molecular Systems Biology·Rebecka JörnstenSven Nelander
Jun 15, 2010·Molecular Cell·Wenwei HuZhaohui Feng
Sep 27, 2018·Annals of Oncology : Official Journal of the European Society for Medical Oncology·D GłodzikS Nik-Zainal
Jul 1, 2010·Optics Express·Ching-Wei Chang, Mary-Ann Mycek
Jul 13, 2017·BMC Bioinformatics·Eleni Ioanna DelatolaJennifer Wong

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Methods Mentioned

BETA
chromosomal aberrations
chromosomal aberration

Software Mentioned

Rendersome
CGHseg
DNAcopy

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