Method
Detecting transcriptionally active regions using genomic tiling arrays
-
* Corresponding author: Harmen J Bussemaker hjb2004@columbia.edu
1 Department of Biological Sciences, Columbia University, 1212 Amsterdam Avenue, New York, NY, 10027 USA
2 Integrated Program in Cellular, Molecular and Biophysical Studies, Columbia University, 630 w. 168th Street, New York, NY, 10032 USA
3 Bioinformatics Laboratory, Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
4 Department of Genetics, Yale University School of Medicine, 333 Cedar Street, PO Box 208005, New Haven, CT, 06520-8005, USA
5 Department of Ecology and Evolutionary Biology, Yale University, 165 Prospect Street, PO Box 208106, New Haven, CT, 06250-8106, USA
6 Center for Computational Biology and Bioinformatics, Columbia University, 1130 St. Nicholas Avenue, New York, NY, USA
Genome Biology 2006, 7:R59 doi:10.1186/gb-2006-7-7-r59
Published: 19 July 2006Additional files
Additional date file 1:
Probe sequence and raw signal intensities for exon probes
Format: GZ Size: 3.1MB Download file
Additional date file 2:
Probe sequence and raw signal intensities for non-exon probes
Format: GZ Size: 3.4MB Download file
Additional date file 3:
Probe sequence and raw signal intensities for negative control probes
Format: GZ Size: 34KB Download file
Additional date file 4:
Genomic coordinates for regions measured by exon probes
Format: GZ Size: 1.2MB Download file
Additional date file 5:
Genomic coordinates for regions measured by non-exon probes
Format: GZ Size: 1.2MB Download file
Additional date file 6:
Supplementary Figure 1 demonstrates that signal variability between different probe populations on the same channel is not explained by probe sequence composition; supplementary Figure 2 shows Q-Q plots for NCP signal intensities in different channels, showing that these have heterogeneous and non-normal distributions; supplementary Figure 3 demonstrates that signal variability between negative control probes on different channels is not explained by probe sequence composition; supplementary Figure 4 has two ROC curves showing true positive rate versus false positive rate relative to (a) mRNA and (b) EST transcripts annotated in the UCSC database (the '+' symbol corresponds to the transfrags as defined by Cheng et al. [3]; and lines correspond to our algorithm as applied with/without neighborhood smoothing and with/without minrun/maxgap post-processing)
Format: PDF Size: 777KB Download file
This file can be viewed with: Adobe Acrobat Reader