We described a novel Topology-based pathway enrichment analysis, which integrated the global position of the nodes and the topological property of the pathways in Kyoto Encyclopedia of Genes and Genomes Database. We also provide some functions to obtain the latest information about pathways to finish pathway enrichment analysis using this method.
|Date of publication||2017-01-03 07:33:51|
|Maintainer||Wei Jiang <firstname.lastname@example.org>|
all_genes: All human protein coding genes
AUCSC: Calculate the area under the cumulative enrichment curve...
DownloadKGML: Download the latest KGML files
filterNode: Filter the nodes in pathways
gene2ec: The relationship of genes and EC
gene2ko: The relationship of genes and KO
getEntry: Obtain the nodes
getGeneFromEnzyme: Obtain the genes from enzymes
getGeneFromKGene: Obtain the genes from KGenes
getGeneFromKO: Obtain the genes from KO
getGraphics: Recontructe the network based on pathways
getKGeneFromEnzyme: Obtain genes from KGnenes
getKGeneFromKO: Obtain the genes from KO
getNonMetabolicGraph: Convert the non-metaboloc pathway to network
getOrgAndIdType: Get the type names of nodes
getPathway: Get the pathway from KEGG database.
getProduct: Get the products
getReaction: Get the reaction of nodes in pathways
getRelation: Get the relation of nodes in pathways
getSimpleGraph: Obtain the graph of pathways
getSubstrate: Obtain the information about nodes in KEGG database
getSubtype: Get the type of nodes
getUGraph: Obtain the graph of pathways
getUnknowProduct: Get the products
getUnknowReaction: Get the reaction of nodes in pathways
getUnknowRelation: Get the relation of nodes in pathways
getUnknowSubstrate: Obtain the information about nodes in KEGG database
getUnknowSubtype: Obtain the types of genes in pathways
importLatesData: Import the latest relationship information.
keggGene2gene: KeggGene to genes
mapNode: Obtain the relationship of nodes and genes
node_gene: The relationship between nodes and genes
NodeGene: Restract the relationship between nodes and genes.
NodeGeneData: Intergate list of node,gene and the score of node.
num_node_gene_score: The score of each node in a certain pathway
PathNetwork: Reconstruct pathways to networks
pathway_names: Pathway names in KEGG Database
simplifyGraph: Recontructe the network based on pathways
TPEA: Statistical test and calculate the significance
TPEA-package: TPEA: A novel topology-based pathway enrichment analysis...
UPDATE: Update the latest data from KEGG database
ViewLatestTime: Check up the latest date of KGML files
viewpathway: The visualization of interested pathway based on the genes...