cancer prognosis

Integrated Genomic Analysis of the Ubiquitin Pathway across Cancer Types

Protein ubiquitination is a dynamic and reversibleprocess of adding single ubiquitin molecules orvarious ubiquitin chains to target proteins. Here,using multidimensional omic data of 9,125 tumorsamples across 33 cancer types from The CancerGenome Atlas, we perform comprehensive molecu-lar characterization of 929 ubiquitin-related genesand 95 deubiquitinase genes. Among them, we sys-tematically identify top somatic driver candidates,including mutatedFBXW7with cancer-type-specificpatterns and amplifiedMDM2showing a mutuallyexclusive pattern withBRAFmutations.

Response to: comment on “Impact of tumor site on the prognosis of small bowel adenocarcinoma”

To test the validity of the model and answer the second question by Wang et al.,2 considering the small sample of the population, we implemented the analysis including the cross-validation with bootstrapping. To quantify the discrimination performance of the model, Harrell’s C-index was measured. The model was subjected to bootstrapping validation (1000 bootstrap resamples) to calculate the optimistic corrected estimate of C-index. The C-index for OS models was 0.70 while the corrected C-index was 0.67. Despite the small sample, the conclusions of our model seem to be robust.

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