What is OncoScape?
OncoScape is a package for cancer gene prioritization for the R statistical programming environment. It compares molecular profiling data of two groups of samples in order to identify genes that show significant differences between these groups. Currently, OncoScape performs an analysis of the following five data types:
- Gene Expression
- DNA Copy Number
- DNA Methylation
- mutation
- shRNA knock-down data
Aberrations in each gene are called for each data type separately and scored as 0 (no significant difference found) or 1 (significant difference found). These scores are summed across all data types giving the final score. OncoScape differentiates between activating (oncogene-like) and inactivating (tumor suppressor-like) aberrations and calculates independent scores for both directions, the oncogene score and tumor suppressor score, respectively. Furthermore, a combined score is calculated as oncogene score minus tumor suppressor score. OncoScape can be applied to the comparison of any arbitrary groups of samples, such as:
- tumors vs. normals
- cell lines vs. normals
- samples sensitive to treatment vs resistant ones
- samples with mutations in gene X vs wild type ones
- different cancer subtypes
Browse existing results
We have performed a comprehensive analysis of tumor samples from 11 cancer types and cell lines from 10 cancer types. Tumor data was obtained from The Cancer Genome Atlas (TCGA) and cell line data from the Cancer Cell Line Encyclopedia (CCLE). The results can be explored using OncoScapeWeb. In addition, all results of our analyzes are publicly accessible in Synapse (Synapse accession doi:10.7303/syn2518467).
Run OncoScape
The source code is available on GitHub. The manuscript is available on BioRXiv.
Publications
If you use OncoScape in your work, please cite:
Schlicker, A. et al. OncoScape: Exploring the cancer aberration landscape by genomic data fusion. Sci. Rep. 6, 28103 (2016).