mirIntegrator (version 1.2.0)

augmented_pathways: Signaling pathways augmented with miRNA.

Description

Human signaling KEGG pathways augmented with validated miRNA-target interactions from mirTarBase using the mirIntegrator package. These interactions represent the biological miRNA repression over its target genes and are included in the model as negative links.

Usage

data("augmented_pathways")

Value

A list of graphNEL objects where each graph is a pathway that were augmented with miRNA-target interactions. The name of each pathway is its KEGG pathway identifier.

Source

Generated using the mirIntegrator package. A script that constructs the augmented_pathways object may be found in 'inst/scripts/get_augmented_pathways.R', see the example.

References

M. Kanehisa and S. Goto, KEGG: Kyoto Encyclopedia of Genes and Genomes, Nucleic Acids Research, vol. 28, pp. 27-30, January 2000.

S.-D. Hsu, Y.-T. Tseng, S. Shrestha, Y.-L. Lin, A. Khaleel, C.-H. Chou, C.-F. Chu, H.-Y. Huang, C.-M. Lin, S.-Y. Ho, T.-Y. Jian, F.-M. Lin, T.-H. Chang, S.-L. Weng, K.-W. Liao, I.-E. Liao, C.-C. Liu, and H.-D. Huang, miRTarBase update 2014: an information resource for experimentally validated miRNA-target interactions, Nucleic Acids Research, vol. 42, pp. D78 - D85, Jan. 2014.

See Also

mirTarBase and kegg_pathways

Examples

data(augmented_pathways)
head(augmented_pathways)

script <- system.file("scripts", "get_augmented_pathways.R", 
                      package = "mirIntegrator")
script
readLines(script)