Method
An improved method for detecting and delineating genomic regions with altered gene expression in cancer
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* Corresponding author: Björn Nilsson bjorn.nilsson@med.lu.se
1 Department of Clinical Genetics, Lund University Hospital, SE-221 85 Lund, Sweden
2 Department of Transfusion Medicine, Lund University Hospital, SE-221 85 Lund, Sweden
3 Imaging Platform, Broad Institute of Harvard University and MIT, Cambridge, MA 02142, USA
4 Department of Automatic Control, Royal Institute of Technology, SE-100 44 Stockholm, Sweden
5 Department of Applied Mathematics, Malmö University, Malmö, SE-205 06 Malmö, Sweden
6 Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, NY 10021, USA
Genome Biology 2008, 9:R13 doi:10.1186/gb-2008-9-1-r13
Published: 21 January 2008Additional files
Additional file 1:
Complete set of ROC curves from the simulation study
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Additional file 2:
Complete set of breakpoint distribution plots from the simulation study
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Additional file 3:
High-resolution versions of the expression maps for each of the ALL cases in the Ross et al data set, as reconstructed by the proposed algorithm. Gray: Original gene scores from the Ross data set. Blue solid: Segmented gene scores. Each row represents one case, except for the bottom row which displays the average segmentation result and DNA copy number profiles (orange) across each leukemic subtype.
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Additional file 4:
Additional information about the proposed segmentation algorithms, including pseudocode.
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Additional file 5:
Additional data illustrating that the use of the default method parameters for CGHseg is appropriate.
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