Mining breast cancer genes with a network based noise-tolerant approach

By Yaling Nie, Jingkai Yu. 2013

17 citations recorded by the source corpus.

BackgroundMining novel breast cancer genes is an important task in breast cancer research. Many approaches prioritize candidate genes based on their similarity to known cancer genes, usually by integrating multiple data sources. However, different types of data often contain varying degrees of noise. For effective data integration, it’s important to design methods that work robustly with respect to noise.ResultsGene Ontology (GO) annotations were often utilized in cancer gene mining works. However, the vast majority of GO annotations were computationally derived, thus not completely accurate. A set of genes annotated with breast cancer enriched GO terms was adopted here as a set of source data with realistic noise. A novel noise tolerant approach was proposed to rank candidate breast cancer genes using noisy source data within the framework of a comprehensive human Protein-Protein Interaction (PPI) network. Performance of the proposed method was quantitatively evaluated by comparing it with the more established random walk approach. Results showed that the proposed method exhibited better performance in ranking known breast cancer genes and higher robustness against data noise than the random walk approach. When noise started to increase, the proposed method was able to maintained relatively stable performance, while the random walk approach showed drastic performance decline; when noise increased to a large extent, the proposed method was still able to achieve better performance than random walk did.ConclusionsA novel noise tolerant method was proposed to mine breast cancer genes. Compared to the well established random walk approach, it showed better performance in correctly ranking cancer genes and worked robustly with respect to noise within source data. To the best of our knowledge, it’s the first such effort to quantitatively analyze noise tolerance between different breast cancer gene mining methods. The sorted gene list can be valuable for breast cancer research. The proposed quantitative noise analysis method may also prove useful for other data integration efforts. It is hoped that the current work can lead to more discussions about influence of data noise on different computational methods for mining disease genes.

Subfields: Molecular Biology

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In Molecular Biology

1. Zhaohui S. Qin
2. Yun Bai
3. Rendong Yang
4. Tianwei Yu

Citations in the corpus

• EgoNet: identification of human disease ego-network modules (2014, methodology): “To date, many computational methods have been developed to integrate gene expression profiles with protein-protein interaction maps or pathway databases, with the goal of identifying significant subnetwork markers for predicting biological or clinical outcomes [10-18].”
• Detecting subnetwork-level dynamic correlations (2017, background): “So far such work has been solely focused feature selection—finding subnetworks that associate with certain disease outcomes (Chen et al., 2013; Ciriello et al., 2012; Nie and Yu, 2013; Sanguinetti et al., 2008; Su et al., 2010; Taylor et al., 2009; Wei and Pan, 2010; Wei and Pan, 2012; Yang et al., ”