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Patient-oriented gene set analysis for cancer mutation data

Simina M Boca1, Kenneth W Kinzler2, Victor E Velculescu2, Bert Vogelstein2 and Giovanni Parmigiani3*

Author Affiliations

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

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Genome Biology 2010, 11:R112  doi:10.1186/gb-2010-11-11-r112

Published: 23 November 2010

Additional files

Additional file 1:

Notations, derivations, and theorems used for the patient-oriented methods.

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Open Data

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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Open Data

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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Open Data

Additional file 4:

Analyses on three more datasets.

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Open Data