R/pathwayTopology.R
retrieve_topology.RdRetrieve pathway topology matrices and convert to normalized weighted directed adjacency matrices describing gene signaling networks.
retrieve_topology(database, pathwayName = NULL, beta = NULL)See example for supported databases.
Optional. Subset of pathway names as a vector.
Optional. A named numeric vector of weights to be assigned to each type of gene/protein relation type. See details for more information.
A list where each element is a matrix corresponding to a pathway
This function takes the pathway topology information retrieved using graphite and convert them to normalized weighted directed adjacency
matrices describing the gene signaling network, which can be directed used to compute pathway perturbation score through SPIA algorithm.
See cited document for more details.
The beta parameter specifies weights to be assigned to each type of gene-gene interaction. It should be a named numeric vector of length 23, whose names must be: c("activation","compound","binding/association","expression","inhibition","activation_phosphorylation","phosphorylation", "indirect","inhibition_phosphorylation","dephosphorylation_inhibition","dissociation","dephosphorylation","activation_dephosphorylation", "state","activation_indirect","inhibition_ubiquination","ubiquination","expression_indirect","indirect_inhibition", "repression","binding/association_phosphorylation","dissociation_phosphorylation","indirect_phosphorylation"). If unspecified, beta will be by default chosen as: c(1,0,0,1,-1,1,0,0,-1,-1,0,0,1,0,1,-1,0,1,-1,-1,0,0,0).
The converted weighted adjacent matrices will be stored in a list. We recommend users to store the returned list as a file so this step only needs to be performed once.
This function only supports and can only be used to retreive human databases as this stage.
Tarca AL, Draghici S, Khatri P, Hassan SS, Mittal P, Kim JS, Kim CJ, Kusanovic JP, Romero R. A novel signaling pathway impact analysis. Bioinformatics. 2009 Jan 1;25(1):75-82. Sales, G., Calura, E., Cavalieri, D. et al. graphite - a Bioconductor package to convert pathway topology to gene network. BMC Bioinformatics 13, 20 (2012).
# \donttest{
# explore all databases supported by graphite
graphite::pathwayDatabases()
#> species database
#> 1 athaliana kegg
#> 2 athaliana pathbank
#> 3 athaliana wikipathways
#> 4 btaurus kegg
#> 5 btaurus pathbank
#> 6 btaurus reactome
#> 7 btaurus wikipathways
#> 8 celegans kegg
#> 9 celegans pathbank
#> 10 celegans reactome
#> 11 celegans wikipathways
#> 12 cfamiliaris kegg
#> 13 cfamiliaris reactome
#> 14 cfamiliaris wikipathways
#> 15 dmelanogaster kegg
#> 16 dmelanogaster pathbank
#> 17 dmelanogaster reactome
#> 18 dmelanogaster wikipathways
#> 19 drerio kegg
#> 20 drerio reactome
#> 21 drerio wikipathways
#> 22 ecoli kegg
#> 23 ecoli pathbank
#> 24 ecoli wikipathways
#> 25 ggallus kegg
#> 26 ggallus reactome
#> 27 ggallus wikipathways
#> 28 hsapiens kegg
#> 29 hsapiens panther
#> 30 hsapiens pathbank
#> 31 hsapiens pharmgkb
#> 32 hsapiens reactome
#> 33 hsapiens smpdb
#> 34 hsapiens wikipathways
#> 35 mmusculus kegg
#> 36 mmusculus pathbank
#> 37 mmusculus reactome
#> 38 mmusculus wikipathways
#> 39 rnorvegicus kegg
#> 40 rnorvegicus pathbank
#> 41 rnorvegicus reactome
#> 42 rnorvegicus wikipathways
#> 43 scerevisiae kegg
#> 44 scerevisiae pathbank
#> 45 scerevisiae reactome
#> 46 scerevisiae wikipathways
#> 47 sscrofa kegg
#> 48 sscrofa reactome
#> 49 sscrofa wikipathways
#> 50 xlaevis kegg
gsTopology <- retrieve_topology(database = "kegg")# }
# if only interested in selected pathways, specify the pathway names in the `pathwayName` parameter
gsTopology <- retrieve_topology(database = "kegg",
pathwayName = c("Glycolysis / Gluconeogenesis",
"Citrate cycle (TCA cycle)","Pentose phosphate pathway"))