Predicting links between tumor samples and genes using 2-Layered graph based diffusion approach

BMC Bioinformatics

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[1] 0000 0004 0488 0789, grid.6142.1, Insight Centre for Data Analytics, National University of Ireland Galway, Galway, Ireland;0000 0004 0488 0789, grid.6142.1, School of Mathematics Statistics and Applied Mathematics, National University of Ireland Galway, Galway, Ireland;

关键词: Graph;    Heat;    Diffusion;    Prediction;    Tumor;    Genes;    Interaction;   

DOI  :  10.1186/s12859-019-3056-2

来源: publisher

【 摘 要 】

BackgroundDetermining the association between tumor sample and the gene is demanding because it requires a high cost for conducting genetic experiments. Thus, the discovered association between tumor sample and gene further requires clinical verification and validation. This entire mechanism is time-consuming and expensive. Due to this issue, predicting the association between tumor samples and genes remain a challenge in biomedicine.ResultsHere we present, a computational model based on a heat diffusion algorithm which can predict the association between tumor samples and genes. We proposed a 2-layered graph. In the first layer, we constructed a graph of tumor samples and genes where these two types of nodes are connected by “hasGene” relationship. In the second layer, the gene nodes are connected by “interaction” relationship. We applied the heat diffusion algorithms in nine different variants of genetic interaction networks extracted from STRING and BioGRID database. The heat diffusion algorithm predicted the links between tumor samples and genes with mean AUC-ROC score of 0.84. This score is obtained by using weighted genetic interactions of fusion or co-occurrence channels from the STRING database. For the unweighted genetic interaction from the BioGRID database, the algorithms predict the links with an AUC-ROC score of 0.74.ConclusionsWe demonstrate that the gene-gene interaction scores could improve the predictive power of the heat diffusion model to predict the links between tumor samples and genes. We showed the efficient runtime of the heat diffusion algorithm in various genetic interaction network. We statistically validated our prediction quality of the links between tumor samples and genes.

【 授权许可】

CC BY