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The same two trinucleotides, 5'-TCA and 5'-TCG, were the most commonly mutated cytosine-containing motifs in two independent breast cancer mutation data sets.
Gene expression, copy number and gene mutation data sets were combined into an integrated data sets.
HotSpotter offers a rapid, easy-to-use method for analyzing one's own and/or publicly available mutation data sets (as shown with the TCGA UCEC data set).
From a viewpoint of clinical use, it is obvious that any mutation analysis platform cannot serve as a useful one without reliable mutation data sets.
So we combined gene expression, copy number and gene mutation data sets into an integrated dataset, and conducted SVM-RFE for feature selection based on the integrated dataset.
This paper presents a method that allows rapid and easy visualization of mutation data sets and identification of potential gene mutation hotspot sites and/or regions.
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As such, we selected to decompose the pooled mutation data set into five stable mutational signatures.
Although our study provided the largest mutation data set for MA line based mutational analysis to date, a much larger survey of mutational variation that includes MA lines derived from many dozens to hundreds of progenitor genotypes will be required to more broadly and effectively address the extent of mutational variation within and between related animal species.
We focus on a cancer mutation data set of human kinases from G reenman et al. (2007).
To eliminate self-referential observations, a COSMIC data set devoid of the TCGA UCEC endometrial cancer samples was employed as the reference mutation data set.
Once the LoF and GoF mutation information was collected from the literature, the mutation data set was preprocessed for further analysis.
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