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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.
● Data Source:
BioConductor
● Keywords: datasets, pathway, microRNA, miRNA
● Alias: augmented_pathways
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This function takes each pathway of the input list of signaling pathways and adds the miRNAs that are related to it.
● Data Source:
BioConductor
● Keywords:
● Alias: integrate_mir
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This function creates a pdf file with plottings of a list of augmented pathways.
● Data Source:
BioConductor
● Keywords:
● Alias: pathways2pdf
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Functions for plotting a particular augmented pathway. In the plot, miRNAs that were added to the original pathway are differentiated from proteins that were originally in the pathway. Blue boxes represent the proteins that were part of the original pathway, and black boxes represent the miRNAs that were added during augmentation.
● Data Source:
BioConductor
● Keywords:
● Alias: plot_augmented_pathway
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plot_change
(Package: mirIntegrator) :
Plotting the change in pathways order
Function for plotting a lines plot of the difference in pathways' order. The resultant plot shows the comparison between the order of the original pathways and the order of the augmented pathways. It also contains a line with the order difference (order of the augmented pathways minus order of the original pathways). The order of a biological pathway is the number of genes that are involved in it.
● Data Source:
BioConductor
● Keywords:
● Alias: plot_change
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Find the pathway with the fewer number of nodes among a list of pathways. This simple function is an example of how to navigate the genes on a list of pathways.
● Data Source:
BioConductor
● Keywords:
● Alias: smallest_pathway
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providing 
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