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In order to validate our results showing heterogeneous distribution of BRAF-M% in mutated melanoma tumors, we investigated the next-generation sequenced DNA mutation data of the 104 mutated skin melanomas in the TCGA database.
We projected the gene mutation data of the 2740 TCGA tumor samples onto the map.
We next downloaded mutation data of a cohort of GBMs [ 6].
In this study, we separated the mutation data of TSGs and OCGs from the rest genes and performed a comparison of five gene sets.
We used a dataset and the software provided by the authors to reconstruct a hierarchical clustering on somatic mutation data of ovarian cancer samples.
In addition, we matched the readily filtered mutational data of 38 MM, published in the supplements of Chapman et al. with the mutation data of our cases.
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Specifically, pedigree analysis has provided substantial amounts of mutation data for broad ranges of chromosomal loci and organisms [ 8- 10].
We analyzed our mutation data for evidence of over- or underenrichment of mutations in COGs genes that share a common function.
The point mutation status of a gene was defined for each sample by querying the point mutation data for each pair of sample ID and Ensembl gene ID.
We proposed an integrative model by combining gene expression data and mutation data to improve the performance of the MOGA algorithm in a biological context.
The analysis of mutation rates for 4 bp contexts analysis requires large amounts of mutation data (millions of inferred mutations) to provide statistically significant and biologically meaningful results.
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