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For better understanding these functional interactions among cancer genes, this study presents a systems biology approach and conducts a comprehensive analysis of cancer genes with co-occurring mutations and anti-co-occurring mutations.
The AD values for genes with co-occurring mutations, genes with anti-co-occurring mutations, and random gene pairs were then compared.
Co-occurring mutated genes were first mapped into 183 human signaling pathways, and 42 pairs of genes with co-occurring mutations were mapped to the same pathways.
Genes with co-occurring mutations tend to have similar mutation frequencies, whereas genes with anti-co-occurring mutations tend to have different mutation frequencies.
It was also revealed that genes with co-occurring mutations tend to have similar mutation frequencies, whereas genes with anti-co-occurring mutations tend to have different mutation frequencies.
Genes with co-occurring mutations were found to have smaller AD values than genes with anti-co-occurring mutations (P = 3.32×10−7, Wilcoxon test, Figure 3A).
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The clinical features of individuals with two mutations were distinct from and/or more severe than those of individuals carrying only the co-occurring mutation.
Mutations of certain cancer genes tend to co-occur (termed co-occurring mutation in this work), suggesting that they may contribute together to tumor formation and development.
Certain cancer genes contribute to tumorigenesis in a manner of either co-occurring or mutually exclusive (anti-co-occurring) mutations; however, the global picture of when, where and how these functional interactions occur remains unclear.
Coexisting mutations of KRAS/ BRAF and PIK3CA have been reported in several studies [ 24, 30, 31, 36], with PIK3CA exon 20 mutations more frequently co-occurring with mutations of unknown significance or with KRAS codon 146 mutations [ 24].
Although some cancer genes with co-occurring and anti-co-occurring mutations have been revealed, the complexity of human cancer gene mutations prevents us from gaining a global landscape of cancer gene co-occurring and anti-co-occurring mutations.
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