Waiting for Gene List
(More detailed instructions can be found on the instructions/about page.)
This program draws from one or more selected background networks. It will take a list of genes you provide as seed genes and identify all interacting genes that fall on paths through the background network(s) between them.
1. Specify your gene list or query pubmed for a gene list. If you choose to query pubmed it is best to complete steps 2-5 first. This list consists of primary human entrez gene symbols which will be used to find interacting nodes. If you do not specify a valid gene symbol it will not be used. Alternatively you can view connections for one gene of interest using the nearest neighbor function.
2. Select one or more functional association types to use for generating the background network. Information regarding these types is available on the instructions/about page. Be aware that selecting many functional associations will increase the computing time of your result. Each color to the right of a functional association type corresponds to the edge color in the result network.
3. Select Max Path Length. This is the number of steps to search to find intermediate nodes on paths connecting the seed nodes. A value of 1 will only return connections between seed nodes.
4. Choose a cutoff for significance for labeling graph nodes. A z-score is calculated for each intermediate node based on the number of links to the seed nodes and the number of total links it has in the background network. Nodes above this specified threshold will be labeled in a different color.
5. Choose colors for graph nodes based on whether or not it is in the seed list or above the significance threshold.
Sample pubmed query - leukemia , Sample seed gene list - genes associated with eye color