Inferring subgroup specific driver genes from heterogeneous cancer samples via subspace learning with subgroup indication.

Inferring subgroup specific driver genes from heterogeneous cancer samples via subspace learning with subgroup indication.

Publication date: Oct 18, 2019

Detecting driver genes from gene mutation data is a fundamental task for tumorigenesis research. Due to the fact that cancer is a heterogeneous disease with various subgroups, subgroup specific driver genes are the key factors in the development of precision medicine for heterogeneous cancer. However, the existing driver gene detection methods are not designed to identify subgroup specificities of their detected driver genes, and therefore cannot indicate which group of patients are associated with the detected driver genes, which is difficult to provide specifically clinical guidance for individual patients.

By incorporating the subspace learning framework, we propose a novel bioinformatics method called DriverSub, which can efficiently predict subgroup specific driver genes in the situation where the subgroup annotations are not available. When evaluated by simulation datasets with known ground truth and compared with existing methods, DriverSub yields the best prediction of driver genes and the inference of their related subgroups. When we apply DriverSub on the mutation data of real heterogeneous cancers, we can observe that the predicted results of DriverSub are highly enriched for experimentally validated known driver genes. Moreover, the subgroups inferred by DriverSub are significantly associated with the annotated molecular subgroups, indicating its capability of predicting subgroup specific driver genes.

The source code are publicly available at https://github.com/JianingXi/DriverSub.

Supplementary data are available at Bioinformatics online.

Xi, J., Yuan, X., Wang, M., Li, A., Li, X., and Huang, Q. Inferring subgroup specific driver genes from heterogeneous cancer samples via subspace learning with subgroup indication. 05601. 2019 Bioinformatics.

Concepts Keywords
Cancer Real heterogeneous cancers
Inference Group theory
Mutation Subgroup
Simulation Cancer
Subgroup Carcinogenesis
Subspace Simulation
Tumorigenesis

Semantics

Type Source Name
drug DRUGBANK Coenzyme M
disease MESH development
disease MESH tumorigenesis
gene UNIPROT KCNK3
disease DOID cancer
disease MESH cancer

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