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)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
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> library(mirIntegrator)

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/mirIntegrator/augmented_pathways.Rd_%03d_medium.png", width=480, height=480)
> ### Name: augmented_pathways
> ### Title: Signaling pathways augmented with miRNA.
> ### Aliases: augmented_pathways
> ### Keywords: datasets, pathway, microRNA, miRNA
> 
> ### ** Examples
> 
> data(augmented_pathways)
> head(augmented_pathways)
$`path:hsa03008`
A graphNEL graph with directed edges
Number of Nodes = 185 
Number of Edges = 249 

$`path:hsa03013`
A graphNEL graph with directed edges
Number of Nodes = 327 
Number of Edges = 957 

$`path:hsa03015`
A graphNEL graph with directed edges
Number of Nodes = 200 
Number of Edges = 476 

$`path:hsa03018`
A graphNEL graph with directed edges
Number of Nodes = 186 
Number of Edges = 335 

$`path:hsa03320`
A graphNEL graph with directed edges
Number of Nodes = 149 
Number of Edges = 414 

$`path:hsa03460`
A graphNEL graph with directed edges
Number of Nodes = 122 
Number of Edges = 211 

> 
> script <- system.file("scripts", "get_augmented_pathways.R", 
+                       package = "mirIntegrator")
> script
[1] "/home/ddbj/local/lib64/R/library/mirIntegrator/scripts/get_augmented_pathways.R"
> readLines(script)
 [1] "# The following script constructs the augmented_pathways dataset"
 [2] "# included in the mirIntegrator package. "                       
 [3] "# This dataset is included only for demostration purposes."      
 [4] ""                                                                
 [5] "require("mirIntegrator")"                                      
 [6] "data(mirTarBase)"                                                
 [7] "data(kegg_pathways)"                                             
 [8] "augmented_pathways <- integrate_mir(kegg_pathways, mirTarBase)  "
 [9] ""                                                                
[10] "save(augmented_pathways, file = "augmented_pathways.rda")"     
[11] "library(tools)"                                                  
[12] "resaveRdaFiles("augmented_pathways.rda")"                      
[13] ""                                                                
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>