- Data Import and Processing
- Clustering and Heatmap Analysis
- Obtaining Networks From a Heatmap and Using GeneConnector
- NetWalk and EF Tables
- FunWalk and FunTables
- Handling and Analyzing Networks
Obtaining Networks From a Heatmap and Using GeneConnector
Networks of molecular relationships can be obtained by exporting a list of genes of interest from a dataset in TableView, by querying the Knowledgebase through Find, by exporting a set of interactions of interest from an Edge Flux Table, or by exporting a set of functional terms from a FunTable. In each case, the corresponding interactions between genes are fetched from the Knowledgebase. Starting from where we left off in the previous section, now we will obtain networks of genes from the clustering we performed at the end of the previous section. Then, we will perform a NetWalk and FunWalk analyses of the dataset, and query them to build networks of genes associated with increased or decreased expression in response to low or high dose doxorubicin (next section).
- In the TableView panel with the heatmap from the previous section, click on the Names column and click button to set this column as gene names. This will match gene names in the column to those in the Knowledgebase and display the number of successfully matched genes.
- Click on row-selection (), and select the cluster of genes that starts with PGF and ends with TP53I3, which corresponds to genes selectively upregulated in low dose but down-regulated in high-dose treatment (see below).
Click on to export the selection to a network view. This will create a network corresponding to the selected genes and all interactions between them in a new NetView window. The resultant network will contain nodes that are disconnected from each other, as there are no direct links between them. In order to understand the network processes these genes are involved in, we need to extract their network context. This can be done by GeneConnector. The GeneConnector will identify genes that are most relevant to the selected genes, and will add them into the network at the same time making sure that the network is not over-crowded (see Manual for more details).
- Before running the GeneConnector and adding additional genes into this network, we need to color these genes in the network so as to distinguish them from new genes that will be added by the GeneConnector. This is done from the Properties window. On the NetView panel, select all nodes in the view. After selecting nodes, you will see in the Properties panel that the Node Color property is showing white. Click on the “…” button next to it and select gray color. Now all the original nodes from the cluster are colored gray, and we are ready to run GeneConnector.
- Select all nodes in the network in the NetViewer window, and click on the GeneConnector button to display the GeneConnector window.
Without making any changes to the default values, press OK. A message dialog will appear saying “11 intermediate nodes will be added to the graph”, press OK. Force the network to do the layout of nodes again by clicking on the combo box that says “Organic layout” and selecting “Organic layout” from the drop down menu. This will redraw the network. Now you will see several white nodes in addition to the gray nodes in the network. You can see that the network is much better connected now (see below).
This is the network corresponding to genes selectively induced by low-dose doxorubicin during cell cycle arrest, but are repressed at high dose doxorubicin during apoptosis. Two of the nodes did not have any neighbors with direct interactions to the gray nodes. However, you can repeat the procedure by selecting all nodes and running the GeneConnector again to connect the remaining two nodes to the main network. Redraw the graph to rearrange the layout, and you will see that now these two nodes are also connected to the main network, though they each have two intermediary nodes (white) connecting them to any other gray node.
One could run GeneConnector using different parameters and options to obtain networks based on the purpose of analysis (see Manual for more details on GeneConnector).
If you click on a node or an interaction, the details of its functional annotations (for a node) or interactions details (for interaction) will be displayed in the Details Window. Panning of the network is done by holding the right mouse button down, and zooming is done by the mouse scroll. Coloring of interactions reflects type of interactions (see section on Handling and analyzing Networks) as shown under “Coloring” () drop-down panel.