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Comprehensive Analysis of Cancer Cell Lines from NCI-60 Cell Lines Panel: Variome, Functional Profile, Phylogenetic and Gene Expression Open Access

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The NCI-60 cell lines panel has providing abundant materials for cancer research. The SNVs detected usually have fundamental influence on cancer development. Through our High-performance Integrated Virtual Environment (HIVE), the SNVs of each cell lines could be thoroughly detected. Using PhyloSNP to build a phylogenetic tree could help to understand the relationship between cancer cell lines. When the SNVs of phylogenetic tree limited to the ones that related to cancer, the effects of cancer-related gene on construct the phylogenetic tree could be easily viewed. Except for the SNVs that related to cancer, the SNVs that could lead to epigenetic change of functional site change also been picked out and used to perform a hierarchical cluster to see the cell lines cluster. To make best advantage of NCI-60 cancer cell lines, we also reviewed the research on gene expression analysis that did cluster analysis as well as the correlation between mRNA and protein expression level. This paper first time builds a phylogenetic tree based on full exome SNVs and cancer-related genes. Also firstly try to research into full exome epigenetic profile, which will encourage more research into the influence of epigenetic change on cancer development.

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