Method
Patient-oriented gene set analysis for cancer mutation data
1 Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, 615 N. Wolfe Street, Baltimore, MD 21205, USA
2 Ludwig Center for Cancer Genetics and Therapeutics and Howard Hughes Medical Institute, Johns Hopkins Kimmel Cancer Center, 1650 Orleans Street, Baltimore, MD 21231, USA
3 Department of Biostatistics, Harvard School of Public Health and Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, 44 Binney Street, Boston, MA 02115, USA
Genome Biology 2010, 11:R112 doi:10.1186/gb-2010-11-11-r112
Published: 23 November 2010Additional files
Additional file 1:
Notations, derivations, and theorems used for the patient-oriented methods.
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Additional file 2:
Cumulative distribution functions (cdf) of P-values for the patient-oriented method with the permutation null without heterogeneity, for 10,000 null samples, using the number of events in the 21 glioblastoma samples from [4].
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Additional file 3:
Comparison of the main patient-oriented methods (passenger null without heterogeneity) to the gene-oriented method on the dataset in [4].
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Additional file 4:
Analyses on three more datasets.
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