title: Construction of a large scale integrated map of macrophage pathogen recognition and effector systems.
abstract: BACKGROUND
  In an effort to better understand the molecular networks that underpin macrophage activation we have been assembling a map of relevant pathways. Manual curation of the published literature was carried out in order to define the components of these pathways and the interactions between them. This information has been assembled into a large integrated directional network and represented graphically using the modified Edinburgh Pathway Notation (mEPN) scheme.
  
  
  RESULTS
  The diagram includes detailed views of the toll-like receptor (TLR) pathways, other pathogen recognition systems, NF-kappa-B, apoptosis, interferon signalling, MAP-kinase cascades, MHC antigen presentation and proteasome assembly, as well as selected views of the transcriptional networks they regulate. The integrated pathway includes a total of 496 unique proteins, the complexes formed between them and the processes in which they are involved. This produces a network of 2,170 nodes connected by 2,553 edges.
  
  
  CONCLUSIONS
  The pathway diagram is a navigable visual aid for displaying a consensus view of the pathway information available for these systems. It is also a valuable resource for computational modelling and aid in the interpretation of functional genomics data. We envisage that this work will be of value to those interested in macrophage biology and also contribute to the ongoing Systems Biology community effort to develop a standard notation scheme for the graphical representation of biological pathways.
authors.affiliation: Division of Pathway Medicine, University of Edinburgh, The Chancellor's Building, College of Medicine, 49 Little France Crescent, Edinburgh EH16 4SB, UK.
authors.forename: Sobia
authors.initials: S
authors.lastname: Raza
authors.forename: Neil
authors.initials: N
authors.lastname: McDerment
authors.forename: Paul A
authors.initials: PA
authors.lastname: Lacaze
authors.forename: Kevin
authors.initials: K
authors.lastname: Robertson
authors.forename: Steven
authors.initials: S
authors.lastname: Watterson
authors.forename: Ying
authors.initials: Y
authors.lastname: Chen
authors.forename: Michael
authors.initials: M
authors.lastname: Chisholm
authors.forename: George
authors.initials: G
authors.lastname: Eleftheriadis
authors.forename: Stephanie
authors.initials: S
authors.lastname: Monk
authors.forename: Maire
authors.initials: M
authors.lastname: O'Sullivan
authors.forename: Arran
authors.initials: A
authors.lastname: Turnbull
authors.forename: Douglas
authors.initials: D
authors.lastname: Roy
authors.forename: Athanasios
authors.initials: A
authors.lastname: Theocharidis
authors.forename: Peter
authors.initials: P
authors.lastname: Ghazal
authors.forename: Tom C
authors.initials: TC
authors.lastname: Freeman
mesh_terms: D001296:Audiovisual Aids; D053263:Gene Regulatory Networks / Q000276:immunology*; D007372:Interferons / Q000378:metabolism; D020935:MAP Kinase Signaling System / Q000502:physiology; D008262:Macrophage Activation / Q000276:immunology*; D016328:NF-kappa B / Q000378:metabolism; D046988:Proteasome Endopeptidase Complex / Q000378:metabolism; D025941:Protein Interaction Mapping / Q000379:methods*; D051193:Toll-Like Receptors / Q000378:metabolism
chemical_list: D016328:NF-kappa B; D051193:Toll-Like Receptors; D007372:Interferons; D046988:Proteasome Endopeptidase Complex
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