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arXiv · 1111.5028

Bootstrap inference for network construction with an application to a breast cancer microarray study

Shuang Li·Li Hsu·Jie Peng·Pei Wang
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Abstract

Gaussian Graphical Models (GGMs) have been used to construct genetic regulatory networks where regularization techniques are widely used since the network inference usually falls into a high-dimension-low-sample-size scenario. Yet, finding the right amount of regularization can be challenging, especially in an unsupervised setting where traditional methods such as BIC or cross-validation often do not work well. In this paper, we propose a new method - Bootstrap Inference for Network COnstruction (BINCO) - to infer networks by directly controlling the false discovery rates (FDRs) of the selected edges. This method fits a mixture model for the distribution of edge selection frequencies to estimate the FDRs, where the selection frequencies are calculated via model aggregation. This method is applicable to a wide range of applications beyond network construction. When we applied our proposed method to building a gene regulatory network with microarray expression breast cancer data, we were able to identify high-confidence edges and well-connected hub genes that could potentially play important roles in understanding the underlying biological processes of breast cancer.

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Shuang Li, Li Hsu, Jie Peng, Pei Wang. 2011-11-21. Bootstrap inference for network construction with an application to a breast cancer microarray study. https://doi.org/10.1214/12-aoas589

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