Description

A list of igraph objects, each object storing a human protein interaction (directed) network for one of 9 data sources. These data sources are downloaded from from Pathway Commons (version 7; a comprehensive collection of public biological interactions/pathways from multiple data sources). Data sources are: 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 the pooled version of this network, please refer to org.Hs.PCommons_DN.

Usage

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

Value

A list of igraph objects. For details about the object of class "igraph", please 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.source <- dRDataLoader(RData.customised='org.Hs.PCommons_DN.source')

Error in dRDataLoader(RData.customised = "org.Hs.PCommons_DN.source"): unused argument (RData.customised = "org.Hs.PCommons_DN.source")
names(org.Hs.PCommons_DN.source)

Error in eval(expr, envir, enclos): object 'org.Hs.PCommons_DN.source' not found
org.Hs.PCommons_DN.source$KEGG

Error in eval(expr, envir, enclos): object 'org.Hs.PCommons_DN.source' not found