compileGRN: Compilation of a gene regulatory network from pathway...

In lgeistlinger/EnrichmentBrowser: Seamless navigation through combined results of set-based and network-based enrichment analysis

Compilation of a gene regulatory network from pathway databases

Description

To perform network-based enrichment analysis a gene regulatory network (GRN) is required. There are well-studied processes and organisms for which comprehensive and well-annotated regulatory networks are available, e.g. the RegulonDB for E. coli and Yeastract for S. cerevisiae. However, in many cases such a network is missing. A first simple workaround is to compile a network from regulations in pathway databases such as KEGG.

Usage

compileGRN(
  org,
  db = "kegg",
  act.inh = TRUE,
  map2entrez = TRUE,
  keep.type = FALSE,
  kegg.native = FALSE
)

Arguments

org	An organism in KEGG three letter code, e.g. ‘hsa’ for ‘Homo sapiens’. Alternatively, and mainly for backward compatibility, this can also be either a list of KEGGPathway objects or an absolute file path of a zip compressed archive of pathway xml files in KGML format.
db	Pathway database. This should be one or more DBs out of 'kegg', 'reactome', 'pathbank', and 'wikipathways'. See pathwayDatabases for available DBs of the respective organism. Default is 'kegg'. Note: when dealing with non-model organisms, GRN compilation is currently only supported directly from KEGG (the argument kegg.native should accordingly be set to TRUE).
act.inh	Should gene regulatory interactions be classified as activating (+) or inhibiting (-)? If TRUE, this will drop interactions for which such a classification cannot be made (e.g. binding events). Otherwise, all interactions found in the pathway DB will be included. Default is TRUE.
map2entrez	Should gene identifiers be mapped to NCBI Entrez Gene IDs? This only applies to Reactome and PathBank as they both use UNIPROT IDs. This is typically recommended when using the GRN for network-based enrichment analysis with the EnrichmentBrowser. Default is TRUE.
keep.type	Should the original interaction type descriptions be kept? If TRUE, this will keep the long description of interaction types as found in the original KGML and BioPax pathway files. Default is FALSE.
kegg.native	For KEGG: should the GRN be compiled from the native KGML files or should graphite's pathway topology conversion be used? See the vignette of the graphite package for details. This is mostly for backward compatibility. Default is FALSE. Note: when dealing with non-model organisms (not supported by graphite) this argument should be set to TRUE.

Value

The GRN in plain matrix format. Two columns named FROM (the regulator) and TO (the regulated gene) are guaranteed. Additional columns, named TYPE and LONG.TYPE, are included if option act.inh or keep.type is activated.

Author(s)

Ludwig Geistlinger

See Also

pathwayDatabases, pathways, KEGGPathway, parseKGML, downloadPathways

Examples

    kegg.grn <- compileGRN(org="hsa", db="kegg")

lgeistlinger/EnrichmentBrowser documentation built on May 9, 2024, 7:22 p.m.