Routines for identifying metabolic subpathways mediated by microRNAs (miRNAs) through topologically locating miRNAs and genes within reconstructed Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathway graphs embedded by miRNAs. (1) This package can obtain the reconstructed KEGG metabolic pathway graphs with genes and miRNAs as nodes, through converting KEGG metabolic pathways to graphs with genes as nodes and compounds as edges, and then integrating miRNA-target interactions verified by low-throughput experiments from four databases (TarBase, miRecords, mirTarBase and miR2Disease) into converted pathway graphs. (2) This package can locate metabolic subpathways mediated by miRNAs by topologically analyzing the "lenient distance" of miRNAs and genes within reconstructed KEGG metabolic pathway graphs.(3) This package can identify significantly enriched miRNA-mediated metabolic subpathways based on located subpathways by hypergenomic test. (4) This package can support six species for metabolic subpathway identification, such as caenorhabditis elegans, drosophila melanogaster, danio rerio, homo sapiens, mus musculus and rattus norvegicus, and user only need to update interested organism-specific environment variables.
|Author||Li Feng, Chunquan Li and Xia Li|
|Bioconductor views||Annotation Graphs MicroRNAs Statistics SubPathways|
|Date of publication||2015-05-20 14:15:38|
|Maintainer||Li Feng <email@example.com>|
|License||GPL (>= 2)|
getBackground: Get the background of molecules
getInteGraphList: Get the reconstructed metabolic pathway graphs
GetK2riData: Get the environment data
getLocSubGraph: Get the located metabolic subpathways
identifyGraph: Annotate and identify subpathways
initializeK2ri: Initialize environment variable k2ri
plotGraph: Visualize a pathway graph
printGraph: Print the results of graph annotation and identification
SubpathwayGMir-internal: SubpathwayGMir internal functions
SubpathwayGMir-package: The SubpathwayGMir package
updateOrgEnvir: Update the organism-specific environment variables
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.