期刊
COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE
卷 128, 期 -, 页码 69-74出版社
ELSEVIER IRELAND LTD
DOI: 10.1016/j.cmpb.2016.02.011
关键词
Integrative; Simulation; Clustering; NMF
类别
资金
- National Institute of Health [R21 CA182715]
- University of Kansas Cancer Center [P30 CA168524]
Background and objective: Integrative approaches for the study of biological systems have gained popularity in the realm of statistical genomics. For example, The Cancer Genome Atlas (TCGA) has applied integrative clustering methodologies to various cancer types to determine molecular subtypes within a given cancer histology. In order to adequately compare integrative or systems-biology-type methods, realistic and related datasets are needed to assess the methods. This involves simulating multiple types of 'omic data with realistic correlation between features of the same type (e.g., gene expression for genes in a pathway) and across data types (e.g., gene silencing involving DNA methylation and gene expression). Methods: We present the software application tool InterSIM for simulating multiple interrelated data types with realistic intra- and inter-relationships based on the DNA methylation, mRNA gene expression, and protein expression from the TCGA ovarian cancer study. Results: The resulting simulated datasets can be used to assess and compare the operating characteristics of newly developed integrative bioinformatics methods to existing methods. Application of InterSIM is presented with an example of heatmaps of the simulated datasets. Conclusions: InterSIM allows researchers to evaluate and test new integrative methods with realistically simulated interrelated genomic datasets. The software tool InterSIM is implemented in R and is freely available from CRAN. (C) 2016 Elsevier Ireland Ltd. All rights reserved.
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