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Construction of a large scale integrated map of macrophage pathogen recognition and effector systems

Sobia Raza12, Neil McDerment12, Paul A Lacaze1, Kevin Robertson13, Steven Watterson13, Ying Chen1, Michael Chisholm1, George Eleftheriadis1, Stephanie Monk1, Maire O'Sullivan1, Arran Turnbull1, Douglas Roy1, Athanasios Theocharidis12, Peter Ghazal13 and Tom C Freeman12*

Author Affiliations

1 Division of Pathway Medicine, University of Edinburgh, The Chancellor's Building, College of Medicine, 49 Little France Crescent, Edinburgh EH16 4SB, UK

2 The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Roslin, Midlothian EH25 9PS, UK

3 Centre for Systems Biology, University of Edinburgh, Darwin Building, King's Building Campus, Mayfield Road, Edinburgh EH9 3JU, UK

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BMC Systems Biology 2010, 4:63  doi:10.1186/1752-0509-4-63

Published: 14 May 2010

Additional files

Additional file 1:

Integrated Map of Macrophage Pathways_graphml-Version. This file can be opened, viewed and edited by users using the freely available graph-editor software yEd (yFiles software, Tubingen, Germany). yEd can be downloaded at webcite where full downloading instructions are described. PubMed IDs supporting the interactions of the pathway are stored on appropriate edges and nodes within this .graphml file. Once an edge is selected the PubMed ID may be viewed within the descriptions tab of the properties box for that edge or node. Individual proteins have a url link to their Entrez gene entry. Furthermore some (complicated) processes also have additional notes to describe the events and can be found under the description tab of properties and when hovering over the node.

Format: ZIP Size: 283KB Download file

Open Data

Additional file 2:

List of Pathway Interactions and Supporting Publications. Interactions included in the pathway map are listed. Official HGNC (human gene nomenclature committee) gene symbols are used to name the interacting components and Entrez gene IDs are also provided. Interacting components are named as individual genes/proteins and also as they appear on the pathway where they may be interacting as part of a protein complex or with a modification (e.g. Phosphorylation). Interactions are described as they appear on the pathway, sub-cellular location and the NCBI-PubMed ID for supporting literature is provided. There are also columns to incorporate additional information (cell type, analytic method etc) where possible.

Format: XLS Size: 1.2MB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 3:

Integrated Map of Macrophage Pathways_pdf-Version. A high resolution .pdf file for viewing the integrated map of macrophage pathways.

Format: PDF Size: 15MB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 4:

Integrated Map of Macrophage Pathways_html-Version. A high resolution flash .html version of the integrated macrophage pathway for viewing in a web browser.

Format: ZIP Size: 1MB Download file

Open Data

Additional file 5:

Integrated Map of Macrophage Pathways in 3D-or-2D View. The integrated macrophage pathway can be viewed in the network visualisation tool BioLayout Express3D, in both 2 and 3-dimentions and also using the original graph co-ordinates as the .graphml file. By choosing the appropriate class-type (found within class tab of graph properties box) the nodes can be coloured according to assigned classes. By default nodes are coloured and shaped according to "node-type" (e.g. proteins, genes, complexes, process nodes) using a 3D-notation scheme described at webcite. Nodes may also be coloured according to sub-cellular location by assigning the "Cellular location" class. It is also possible to import other class-sets of interest; for example information about a components regulation/behaviour in a dataset. Within BioLayout Express3D one can easily follow the flow of information through the pathway by selecting parent or children nodes of a component of interest to highlight them. BioLayout Express3D software is freely available and can be downloaded at webcite

Format: ZIP Size: 94KB Download file

Open Data

Additional file 6:

Overlay of Ifn-β Regulated Targets onto the Integrated Map of Macrophage Pathways. Components within clusters of co-ordinately expressed transcripts following Ifn-β stimulation were exported as class sets from a mouse expression graph generated in BioLayout Express3D and imported onto the 'human' macrophage pathway diagram (.layout file) within BioLayout Express3D. Pathway components that are regulated by Ifn-β are enlarged and coloured according to their behaviour within the dataset and all other nodes are coloured grey, in this way allowing the easy identification and visualisation of regulated components. BioLayout Express3D software is freely available and can be downloaded at webcite

Format: ZIP Size: 94KB Download file

Open Data