Mapping biological process relationships and disease perturbations within a pathway network - main results
Description
Set cover The subset of pathways generated by the set cover, covering 100% of the genes and 99.95% of the genes are given in the tab delimited files are given by the set cover files. Semantic distances The 'all edges' file provides semantic distances in a text delimited file. One indicate the highest level of semantic similarity, lower numbers show reduced similarity. Disease/ drug strings list the terms used to filter for drug and disease terms Cancer pathways All cancer related pathways are supplied 'all cancer pathways.txt' The sample of cancers used in figure 9 are in 'cancer pathway nodes.txt'. The GI and leukemia pathways in figure 10 are in 'cancer GI pathways.txt' and 'cancer leukemia pathways.txt'. These files are formated as node annotations for use with the multicolored nodes plugin. Network files 'pathway network.cys' is a cytoscape file created in cytoscape 2.7 'edges bma wang.txt' contains the pathways used to generate the file 'functionally annotated in network.txt' contains the GO sample used in Figure 6. The file is formated as node annotations for use with the multicolored nodes plugin.