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论文题目: Identification of HPV Integration and Gene Mutation in HeLa Cell Line by Integrated Analysis of RNA-Seq and MS/MS Data
英文论文题目: Identification of HPV Integration and Gene Mutation in HeLa Cell Line by Integrated Analysis of RNA-Seq and MS/MS Data
第一作者: Sun, H; Chen, C; Lian, BF; Zhang, MH; Wang, XJ; Zhang, B; Li, YX; Yang, PY; Xie, L
英文第一作者: Sun, H; Chen, C; Lian, BF; Zhang, MH; Wang, XJ; Zhang, B; Li, YX; Yang, PY; Xie, L
联系作者: Xie, L (reprint author), Shanghai Acad Sci & Technol, Shanghai Ctr Bioinformat Technol, 1278 Ke Yuan Rd, Shanghai 201203, Peoples R China.
英文联系作者: Xie, L (reprint author), Shanghai Acad Sci & Technol, Shanghai Ctr Bioinformat Technol, 1278 Ke Yuan Rd, Shanghai 201203, Peoples R China.
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发表年度: 2015
卷: 14
期: 4
页码: 1678-1686
摘要: HeLa cell line, which was derived from cervical carcinoma, provides an idea platform to study both the integration of human papillomavirus and the massive mutations occurring on the cancer cell genome. Proteogenomics is a field with the intersection of proteomics and genomics to perform gene annotation and identify gene mutation. In this work, we first identified the SNV/INDEL, structural variation (SV), and virus infection/integration events from RNA-Seq data of HeLa cell line; then, by applying proteogenomics strategy, we were able to detect some of the genomic events with the tandem mass spectrometry (MS/MS) data from the same sample. Furthermore, some of the mutated peptides were experimentally validated using multiple reaction monitoring technology. The integrated analysis of the RNA-Seq and MS/MS data not only renders the discovery of HeLa cell genome variations more credible but also illustrates a practical workflow for protein-coding mutation discovery in cancer-related studies.
英文摘要: HeLa cell line, which was derived from cervical carcinoma, provides an idea platform to study both the integration of human papillomavirus and the massive mutations occurring on the cancer cell genome. Proteogenomics is a field with the intersection of proteomics and genomics to perform gene annotation and identify gene mutation. In this work, we first identified the SNV/INDEL, structural variation (SV), and virus infection/integration events from RNA-Seq data of HeLa cell line; then, by applying proteogenomics strategy, we were able to detect some of the genomic events with the tandem mass spectrometry (MS/MS) data from the same sample. Furthermore, some of the mutated peptides were experimentally validated using multiple reaction monitoring technology. The integrated analysis of the RNA-Seq and MS/MS data not only renders the discovery of HeLa cell genome variations more credible but also illustrates a practical workflow for protein-coding mutation discovery in cancer-related studies.
刊物名称: JOURNAL OF PROTEOME RESEARCH
英文刊物名称: JOURNAL OF PROTEOME RESEARCH
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学科: Biochemistry & Molecular Biology
英文学科: Biochemistry & Molecular Biology
影响因子: 4.245
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论文类别: Article
英文论文类别: Article
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