A logic-based diagram of signalling pathways central to macrophage activation

Sobia Raza¹ , Kevin A Robertson¹^,3 , Paul A Lacaze¹ , David Page¹ , Anton J Enright² , Peter Ghazal¹^,3 and Tom C Freeman¹

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

²Computation and Functional Genomics Laboratory, Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK

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

author email corresponding author email

BMC Systems Biology 2008, 2:36doi:10.1186/1752-0509-2-36


Published:	23 April 2008

Additional files

Additional file 1:

Pathway interaction list. Interactions included in the pathway map are listed (in no particular order) in this data file. Official HGNC (human gene nomenclature committee) gene symbols are used to name the interacting components along with a brief description of the type of interaction and its cellular location. Entrez gene IDs of interacting components are also provided as are the PubMed IDs of the reference(s) supporting each interaction.

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Additional file 2:

Diagram of signalling pathways central to macrophage activation. This file can be opened, viewed and edited by users using the freely available graph-editor software yEd (yFiles software, Tubingen, Germany). This can be downloaded at [22] where full downloading instructions are described. PubMed IDs supporting the interactions of the pathway are stored on appropriate edges within this .graphml yEd file. Once an edge is selected the PubMed ID may be viewed within the descriptions tab of the properties box for that edge.

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Additional file 3:

Bibliography of references supporting interactions on the integrated pathway diagram. Within this document a list of the 282 different references supporting the interactions on the pathway map are provided in alphabetical order (by author name).

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Additional file 4:

Description of the biological content of the pathway. A description of the signalling of the four pathways (Toll-like receptor, interferon, NF-κB and apoptosis) depicted on the integrated pathway diagram is provided here. The interconnectivity of these pathways and their significance in innate immune signalling is also discussed in this section.

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Additional file 5:

Interferon gamma regulated genes. A summary of the analysis of the 58 genes present on both the pathway map and in a transcriptional network of differentially expressed genes following Ifng stimulation. A transcriptional network of all differentially expressed genes (above 1.6 fold change) was constructed and clustered using the graph-based clustering algorithm MCL set at an inflation value of 2.2. This resulted in 26 different clusters, which were then assigned a description of the co-expression pattern they represent over the time course. The cluster numbers and the descriptions of co-expression pattern are shown in this data sheet for the genes present on the pathway diagram. 3 of these genes did not appear in any cluster. Also included in this table is a summary of the gene expression changes according to annova and Empirical Bayes calculations. RMA normalized expression values are included for each gene across the time course as are gene descriptions and GO (gene ontology) annotations for the 58 genes.

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