Revealing common disease mechanisms shared by tumors of different tissues of origin through semantic representation of genomic alterations and topic modeling
作者: Vicky ChenJohn PaisleyXinghua Lu
作者单位: 1University of Pittsburgh
2Columbia University
刊名: BMC Genomics, 2017, Vol.18 (2)
来源数据库: Springer Journal
DOI: 10.1186/s12864-017-3494-z
关键词: CancerTopic modelingSemantic representationCancer genomicsDisease mechanisms
英文摘要: Cancer is a complex disease driven by somatic genomic alterations (SGAs) that perturb signaling pathways and consequently cellular function. Identifying patterns of pathway perturbations would provide insights into common disease mechanisms shared among tumors, which is important for guiding treatment and predicting outcome. However, identifying perturbed pathways is challenging, because different tumors can have the same perturbed pathways that are perturbed by different SGAs. Here, we designed novel semantic representations that capture the functional similarity of distinct SGAs perturbing a common pathway in different tumors. Combining this representation with topic modeling would allow us to identify patterns in altered signaling pathways.
原始语种摘要: Cancer is a complex disease driven by somatic genomic alterations (SGAs) that perturb signaling pathways and consequently cellular function. Identifying patterns of pathway perturbations would provide insights into common disease mechanisms shared among tumors, which is important for guiding treatment and predicting outcome. However, identifying perturbed pathways is challenging, because different tumors can have the same perturbed pathways that are perturbed by different SGAs. Here, we designed novel semantic representations that capture the functional similarity of distinct SGAs perturbing a common pathway in different tumors. Combining this representation with topic modeling would allow us to identify patterns in altered signaling pathways.
全文获取路径: Springer  (合作)
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影响因子:4.397 (2012)

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关键词翻译
关键词翻译
  • representation 表现
  • common 普通
  • modeling 制祝型
  • genomic 染色体组的
  • shared 共享
  • different 不相同的
  • perturb 扰动
  • semantic 语义上的
  • challenging 有希望的
  • functional 功能的