Mapping biological process relationships and disease perturbations within a pathway network - main results

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.

集合覆盖（Set cover）：通过集合覆盖算法生成的通路子集可100%覆盖全部基因，覆盖99.95%基因的子集则存储于制表符分隔的集合覆盖文件中。
语义距离（Semantic distances）："all edges"文件为文本分隔格式的语义距离文件，其中数值1代表最高层级的语义相似性，数值越低则相似性越弱。
疾病/药物词条列表：列出了用于筛选疾病与药物术语的专用词条。
癌症通路（Cancer pathways）：所有癌症相关通路均存储于"all cancer pathways.txt"文件中。用于绘制图9的癌症样本数据集存放在"cancer pathway nodes.txt"内。图10中的胃肠道（GI）通路与白血病通路分别位于"cancer GI pathways.txt"和"cancer leukemia pathways.txt"文件中。上述文件均采用节点注释格式，可配合多色节点插件（multicolored nodes plugin）使用。
网络文件（Network files）："pathway network.cys"为使用Cytoscape 2.7创建的Cytoscape格式文件。"edges bma wang.txt"包含了用于生成"functionally annotated in network.txt"的通路数据。"functionally annotated in network.txt"包含了图6所用的基因本体（Gene Ontology, GO）样本数据，该文件同样采用节点注释格式，可配合多色节点插件使用。