SubpathwayGMir: Identify Metabolic Subpathways Mediated by MicroRNAs

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
Date of publication
2015-05-20 14:15:38
Maintainer
Li Feng <biofengfeng@sina.com>
License
GPL (>= 2)
Version
1.0

View on CRAN

Man pages

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

Files in this package

SubpathwayGMir
SubpathwayGMir/inst
SubpathwayGMir/inst/doc
SubpathwayGMir/inst/doc/SubpathwayGMir.R
SubpathwayGMir/inst/doc/SubpathwayGMir.Rnw
SubpathwayGMir/inst/doc/SubpathwayGMir.pdf
SubpathwayGMir/NAMESPACE
SubpathwayGMir/data
SubpathwayGMir/data/datalist
SubpathwayGMir/data/k2ri.rda
SubpathwayGMir/R
SubpathwayGMir/R/getLocSubGraph.R
SubpathwayGMir/R/identifyGraph.R
SubpathwayGMir/R/getSymbolFromGene.R
SubpathwayGMir/R/updateOrgEnvir.R
SubpathwayGMir/R/getEdgeLty.R
SubpathwayGMir/R/initializeK2ri.R
SubpathwayGMir/R/plotGraph.R
SubpathwayGMir/R/getBackground.R
SubpathwayGMir/R/getInteGraphList.R
SubpathwayGMir/R/getEdgeLabel.R
SubpathwayGMir/R/getOneNodePath.R
SubpathwayGMir/R/fdr.est.R
SubpathwayGMir/R/mytriangle.R
SubpathwayGMir/R/printGraph.R
SubpathwayGMir/R/GetK2riData.R
SubpathwayGMir/R/getLayout.R
SubpathwayGMir/vignettes
SubpathwayGMir/vignettes/SubpathwayGMir.Rnw
SubpathwayGMir/MD5
SubpathwayGMir/build
SubpathwayGMir/build/vignette.rds
SubpathwayGMir/DESCRIPTION
SubpathwayGMir/man
SubpathwayGMir/man/SubpathwayGMir-internal.Rd
SubpathwayGMir/man/getLocSubGraph.Rd
SubpathwayGMir/man/printGraph.Rd
SubpathwayGMir/man/initializeK2ri.Rd
SubpathwayGMir/man/getBackground.Rd
SubpathwayGMir/man/identifyGraph.Rd
SubpathwayGMir/man/plotGraph.Rd
SubpathwayGMir/man/SubpathwayGMir-package.Rd
SubpathwayGMir/man/GetK2riData.Rd
SubpathwayGMir/man/updateOrgEnvir.Rd
SubpathwayGMir/man/getInteGraphList.Rd