2017-03-02
Previous report
Goals
We'd like to learn Recurrent mutations in aspects of
- Distribution of the recurrent mutations
- relationship with
- expression level
- cohorts (or cancer sub types)
- etc
- effects
Distribution
Q. Are recurrent mutations enriched in cancer genes? what about POGs and TSGs
A. Yes they are.
| 1<#<5 | >5 | percent_gt5 | enrich | |
|---|---|---|---|---|
| NON_CG | 261137 | 2999 | 0.0113540 | 1.000000 |
| POG | 5817 | 205 | 0.0340418 | 2.998225 |
| TSG | 6891 | 180 | 0.0254561 | 2.242037 |
*P_value for enrichment are <2.2e-16 by fisher's exact test
Recurrent Mutations and expression
dataset
- Mutation database - TCGA
- Expression database
- TCGA tumor/normal, RNAseq v2 (RSEM)
- patient-level is also available
- CCLE average, microarray*
- used in Mutsigcv (Lawrence et al. 2013)
- TCGA tumor/normal, RNAseq v2 (RSEM)
RNAseq is better than microarray(Mortazavi et al. 2008) CCLE : Cancer Cell Line Encyclopedia
Analysis on a cohort level
An overview of the list
A lack of normal tissue expressions
BRCA is choosed
Gene mRNA expression level in BRCA tumor /normal
expression level in BRCA tumor / CCLE average
*CCLE : Cancer Cell Line Encyclopedia
recurrence(all cancer) ~ expression level in BRCA tumor
Visual check, TP53 as an example
TP53recurrent mutations across cohorts
next plan
next plan
- Todo
- expression level in protein network
- In progress
- other cohorts
- Done
- mutation,expression downloads
- lollipop script refinement
Reference
Lawrence, Michael S., Petar Stojanov, Paz Polak, Gregory V. Kryukov, Kristian Cibulskis, Andrey Sivachenko, Scott L. Carter, et al. 2013. “Mutational Heterogeneity in Cancer and the Search for New Cancer-Associated Genes.” Nature 499 (7457): 214–18. doi:10.1038/nature12213.
Mortazavi, Ali, Brian A. Williams, Kenneth McCue, Lorian Schaeffer, and Barbara Wold. 2008. “Mapping and Quantifying Mammalian Transcriptomes by RNA-Seq.” Nature Methods 5 (7): 621–28. doi:10.1038/nmeth.1226.