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Taken together, our meta-analysis of the various genomic datasets suggest that the epigenomic and genomic landscape of the heterochromatic genes are distinct which could be contributing to their unusual regulatory features as opposed to the surrounding heterochromatin, which is repressive in nature.
We thank Omar Harb, Lucia Peixoto, David Roos, Larry Singh and Sridhar Hannenhalli for useful feedback; Deborah Pinney, Wei Li and Vishal Nayak for help in locating various genomic datasets; Chih-Horng Kuo for providing us with a Babesia-including OrthoMCL clustering.
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In conclusion, we evaluated those restricting factors that hamper integrative analyses of diverse genomic datasets generated by various biomedical technologies, and proposed a simple, flexible and powerful method to overcome these restricting factors.
Beyond the three types of cancers we analyzed, there are many other types of diseases for which various genomic and systematic datasets are available.
Our genomic approach successfully combines various genome-wide datasets and allows the identification of the putative regulatory elements controlling miRNA expression in classically activated macrophages.
Multiple ISWpi1 copies occur at various genomic sites in various Wolbachia genomes [19] [21].
SNF is the state-of-the-art algorithm recently proposed for integrative analyses [ 5], which demonstrates excellent performance in combining multiple genomic datasets to predict subtypes and survival of various cancer patients.
Rice genome projects have generated in depth genomic datasets and a comprehensive set of genomic upstream sequences.
The yeast dataset is provided by Barutcuoglu et al. [ 21] and contains various genomic and proteomic data for 4524 yeast genes.
Such large-scale genomic datasets necessitate powerful tools to link genomic data to its source genome and across genomes.
Fig. 1 Distribution of InDels in various genomic regions.
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