Research
Primary and secondary transcriptional effects in the developing human Down syndrome brain and heart
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* Corresponding author: Jonathan Pevsner pevsner@kennedykrieger.org
1 Program in Biochemistry, Cellular and Molecular Biology, Johns Hopkins School of Medicine, 1830 East Monument Street, Baltimore, MD 21205, USA
2 Department of Neuroscience, Johns Hopkins School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205, USA
3 Partek Incorporated, St Charles, MO 63304, USA
4 Department of Mathematics, Campus Box 1146, Washington University, St Louis, MO 63130, USA
5 Department of Neurology, Kennedy Krieger Institute, 707 North Broadway, Baltimore, MD 21205, USA
6 Pathobiology Graduate Program, Johns Hopkins School of Medicine, 720 Rutland Avenue, Baltimore, MD 21205, USA
7 Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, 615 North Wolfe Street, Baltimore, MD 21205, USA
Genome Biology 2005, 6:R107 doi:10.1186/gb-2005-6-13-r107
Published: 16 December 2005Additional files
Additional data file 1:
Lists information on 25 samples such as race, gender, and postmortem interval.
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Additional data file 2:
This table describes FDR results shown for each individual chromosome.
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Additional data file 3:
Detailed methods for the following topics: Expression data analysis: class prediction; Error estimation using nested cross-validation; Selection of predictor genes for classification; Expression data analysis: functional group testing; and Quantitative real-time PCR. The functional group testing section includes the description of a novel algorithm for functional group analyses.
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Additional data file 4:
Figure legends for the Additional data file 5 and 7 figures.
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Additional data file 5:
This figure shows the results of permutation tests, providing evidence that the functional groups we identified are likely to have been identified with a probability far greater than is expected by chance (as determined by a series of random permutations of the data).
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Additional data file 6:
This table provides results of a Wilcoxon rank test which is appropriate for functional groups having a small size.
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Additional data file 7:
This figure shows a typical quantitative real-time PCR result, in which the level of a transcript is significantly up-regulated in a trisomic sample.
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Additional data file 8:
This table includes oligonucleotide sequences.
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