ellipsoidFN: a tool for identifying a heterogeneous set of cancer biomarkers based on gene expressions.
ellipsoidFN: a tool for identifying a heterogeneous set of cancer biomarkers based on gene expressions.
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ellipsoidFN：一种根据基因表达识别一组异质癌症生物标志物的工具
DOI：
10.1093/nar/gks1288
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发表时间：
2013-02-01
影响因子：
14.9
通讯作者：
Jin Q
中科院分区：
文献类型：
--
作者：
Ren X;Wang Y;Chen L;Zhang XS;Jin Q
通过计算从基因表达谱中识别有效的癌症生物标志物是一项重要且具有挑战性的任务。挑战在于癌症的复杂发病机制，通常涉及许多基因的功能障碍和调控相互作用。因此，迫切需要复杂的分类模型。在这项研究中，我们提出了一种高效的方法，称为椭圆体FN（椭圆体特征网），通过椭圆体对疾病复杂性进行建模并寻找一组异质生物标志物。我们的方法实现了一个非线性分类方案的混合样本的椭球体的概念，并在同一时间使用一个线性规划框架，以有效地选择生物标志物从高维空间。elixoidFN减少了冗余并提高了所鉴定的生物标志物之间的互补性，从而显著增强了癌症和正常样品之间，甚至癌症类型之间的区别性。在真实的前列腺癌、乳腺癌和白血病基因表达数据集上的数值评估表明，ellipsoidFN优于目前最先进的生物标志物识别方法，可以作为未来癌症生物标志物识别的有用工具。ellipsoidFN的Matlab代码可从http://doc.aporc.org/wiki/EllipsoidFN免费获得。
Computationally identifying effective biomarkers for cancers from gene expression profiles is an important and challenging task. The challenge lies in the complicated pathogenesis of cancers that often involve the dysfunction of many genes and regulatory interactions. Thus, sophisticated classification model is in pressing need. In this study, we proposed an efficient approach, called ellipsoidFN (ellipsoid Feature Net), to model the disease complexity by ellipsoids and seek a set of heterogeneous biomarkers. Our approach achieves a non-linear classification scheme for the mixed samples by the ellipsoid concept, and at the same time uses a linear programming framework to efficiently select biomarkers from high-dimensional space. ellipsoidFN reduces the redundancy and improves the complementariness between the identified biomarkers, thus significantly enhancing the distinctiveness between cancers and normal samples, and even between cancer types. Numerical evaluation on real prostate cancer, breast cancer and leukemia gene expression datasets suggested that ellipsoidFN outperforms the state-of-the-art biomarker identification methods, and it can serve as a useful tool for cancer biomarker identification in the future. The Matlab code of ellipsoidFN is freely available from http://doc.aporc.org/wiki/EllipsoidFN.
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