Human protein interaction directed network from Pathway Commons (version 7).

Description

An igraph object that contains a human protein interaction (directed) network. The network is extracted from Pathway Commons (version 7; a comprehensive collection of public biological interactions/pathways from multiple data sources). For each interaction and each relation type, data sources in support are: BIND (see http://bond.unleashedinformatics.com and http://www.ncbi.nlm.nih.gov/pubmed/12519993), BioGRID (see http://thebiogrid.org and http://www.ncbi.nlm.nih.gov/pubmed/16381927), CORUM (see http://mips.helmholtz-muenchen.de/genre/proj/corum and http://www.ncbi.nlm.nih.gov/pubmed/19884131), DIP (see http://dip.doe-mbi.ucla.edu and http://www.ncbi.nlm.nih.gov/pubmed/14681454), HPRD (see http://www.hprd.org and http://www.ncbi.nlm.nih.gov/pubmed/18988627), IntAct (see http://www.ebi.ac.uk/intact and http://www.ncbi.nlm.nih.gov/pubmed/24234451), CTD (see http://ctdbase.org and http://www.ncbi.nlm.nih.gov/pubmed/25326323), HumanCyc (see http://www.humancyc.org and http://www.ncbi.nlm.nih.gov/pubmed/15642094), KEGG (see http://www.genome.jp/kegg and http://www.ncbi.nlm.nih.gov/pubmed/23433509), PANTHER (see http://www.pantherdb.org and http://www.ncbi.nlm.nih.gov/pubmed/23193289), PhosphoSite (see http://www.phosphosite.org and http://www.ncbi.nlm.nih.gov/pubmed/22135298), PID (see http://pid.nci.nih.gov and http://www.ncbi.nlm.nih.gov/pubmed/18832364), Reactome (see http://www.reactome.org and http://www.ncbi.nlm.nih.gov/pubmed/24243840), ReconX (see http://humanmetabolism.org and http://www.ncbi.nlm.nih.gov/pubmed/23455439), TRANSFAC (see http://www.gene-regulation.com and http://www.ncbi.nlm.nih.gov/pubmed/18436575). Only those interactions with directed relations (including relation types: "catalysis_precedes", "controls_expression_of", "controls_phosphorylation_of", "controls_state_change_of" and "controls_transport_of") are retained. For undirected network, please refer to org.Hs.PCommons_UN.

Usage

org.Hs.PCommons_DN <- dRDataLoader(RData = "org.Hs.PCommons_DN")

Value

an object of class "igraph" (see http://igraph.org/r/doc/aaa-igraph-package.html). It has attributes for both vertices and edges. Below are attributes for the vertices:

  • name: gene symbol for the vertices
  • geneid: Entrez geneid for the vertices
  • symbol: gene symbol for the vertices
  • description: gene description for the vertices

Below are attributes for the edges:

  • catalysis_precedes: an integer code indicating support evidence for "catalysis_precedes" relation, that is, the first protein (from) controls a reaction whose output molecule is input to another reaction controled by the second protein (to)
  • controls_expression_of: an integer code indicating support evidence for "controls_expression_of" relation, that is, the first protein (from) controls a conversion or a template reaction that changes expression of the second protein (to)
  • controls_phosphorylation_of: an integer code indicating support evidence for "controls_phosphorylation_of" relation, that is, the first protein (from) controls a reaction that changes the phosphorylation status of the second protein (to)
  • controls_state_change_of: an integer code indicating support evidence for "controls_state_change_of" relation, that is, the first protein (from) controls a reaction that changes the state of the second protein (to)
  • controls_transport_of: an integer code indicating support evidence for "controls_transport_of" relation, that is, the first protein (from) controls a reaction that changes the cellular location of the second protein (to)
  • Notably, there are two supporting evidences: with the PubMed references (assigned with 100), and the number of different data sources. The integer code is the sum of these two. A value of 0 means no supporting evidences. For examples, a value of 105 means that the relation is supported by the PubMed references and by 5 different data sources.

References

Cerami et al. (2011) Pathway Commons, a web resource for biological pathway data. Nucleic Acids Res, 39(Database issue):D685-90.

Examples

org.Hs.PCommons_DN <- dRDataLoader(RData='org.Hs.PCommons_DN')
Error in match.arg(RData): 'arg' should be one of “NA”, “TCGA_mutations”, “ig.DO”, “ig.GOBP”, “ig.GOCC”, “ig.GOMF”, “ig.HPCM”, “ig.HPMA”, “ig.HPMI”, “ig.HPPA”, “ig.MP”, “org.At.eg”, “org.At.egGOBP”, “org.At.egGOCC”, “org.At.egGOMF”, “org.At.egPS”, “org.At.egSF”, “org.At.string”, “org.Ce.eg”, “org.Ce.egGOBP”, “org.Ce.egGOCC”, “org.Ce.egGOMF”, “org.Ce.egPS”, “org.Ce.egSF”, “org.Ce.string”, “org.Da.eg”, “org.Da.egGOBP”, “org.Da.egGOCC”, “org.Da.egGOMF”, “org.Da.egPS”, “org.Da.egSF”, “org.Da.string”, “org.Dm.eg”, “org.Dm.egGOBP”, “org.Dm.egGOCC”, “org.Dm.egGOMF”, “org.Dm.egPS”, “org.Dm.egSF”, “org.Dm.string”, “org.Gg.eg”, “org.Gg.egGOBP”, “org.Gg.egGOCC”, “org.Gg.egGOMF”, “org.Gg.egPS”, “org.Gg.egSF”, “org.Gg.string”, “org.Hs.eg”, “org.Hs.egDGIdb”, “org.Hs.egDO”, “org.Hs.egGOBP”, “org.Hs.egGOCC”, “org.Hs.egGOMF”, “org.Hs.egHPCM”, “org.Hs.egHPMA”, “org.Hs.egHPMI”, “org.Hs.egHPPA”, “org.Hs.egMP”, “org.Hs.egMsigdbC1”, “org.Hs.egMsigdbC2BIOCARTA”, “org.Hs.egMsigdbC2CGP”, “org.Hs.egMsigdbC2CP”, “org.Hs.egMsigdbC2KEGG”, “org.Hs.egMsigdbC2REACTOME”, “org.Hs.egMsigdbC3MIR”, “org.Hs.egMsigdbC3TFT”, “org.Hs.egMsigdbC4CGN”, “org.Hs.egMsigdbC4CM”, “org.Hs.egMsigdbC5BP”, “org.Hs.egMsigdbC5CC”, “org.Hs.egMsigdbC5MF”, “org.Hs.egMsigdbC6”, “org.Hs.egMsigdbC7”, “org.Hs.egMsigdbH”, “org.Hs.egPS”, “org.Hs.egSF”, “org.Hs.string”, “org.Mm.eg”, “org.Mm.egDO”, “org.Mm.egGOBP”, “org.Mm.egGOCC”, “org.Mm.egGOMF”, “org.Mm.egHPCM”, “org.Mm.egHPMA”, “org.Mm.egHPMI”, “org.Mm.egHPPA”, “org.Mm.egMP”, “org.Mm.egPS”, “org.Mm.egSF”, “org.Mm.string”, “org.Rn.eg”, “org.Rn.egGOBP”, “org.Rn.egGOCC”, “org.Rn.egGOMF”, “org.Rn.egPS”, “org.Rn.egSF”, “CLL”, “org.Rn.string”
org.Hs.PCommons_DN
Error in eval(expr, envir, enclos): object 'org.Hs.PCommons_DN' not found