Note: this feature is only available for VisANT2.5 and above
The full format of the expression is shown as following:
(the above data is stored in the file named as mmu.txt)
The format can be simplified, following shows a simplified format:
(above data is part of the data stored in expression_simplest.txt)
Note: any type of data can be imposed over the network, as long as the format is correct.
Expression data can be loaded into VisANT through following menu:
following figure shows the network when mmu.txt is loaded:
Note: Please select correct species (Mus Musculus) before loading the expression data because the expression data itself have no information of the species.
The nodes are identified as Entrez Gene ID in above example and the node color represents the expression value. The actually expression value of the current experiment can be known by moving mouse over the node. The current experiment name is shown in the status bar.
We can pull the detailed information of the nodes using Name Normalization. Make sure that you select case-insensitive for mmu:
Then select all nodes and do name normalization, here is the resulted network
Expression data can be easily be removed from the network through corresponding menu:
The new or matched nodes are selected and colored corresponding to their expression value. The new-added nodes are laid out using a circle.
Note: If the expression data contains nodes that are not in the network, these nodes will be arranged into a circle and put in the cent of the network. To remove these new-added nodes, you can either move whole network into a corner, or group them.
We can also easily mapping expression to the KEGG pathway. To illustrate, clear the network and search for keg pathway map04010, and then load expression data expression_data.TXT, this data file is 8M, and will take about 3 minutes to load. After removing the nodes do not belong to the pathway, the network will look like following (the resulted network has been saved as exp_pathway.xml):
By default the maximum of the expression value is mapped with green color and and minimum value is mapped with red color. The mapping can be changed by clicking on the color button shown below: left for minimum and right for maximum.
If the expression has multiple experiments (which is the case for all expression files), we can simply drag the slider shown in above figure to change the experiments. The name (or the sequential number) of the experiment will be shown at status bar. Click on the empty place of slider will change experiments one by one.
So what we can do if we want to view all expression experiments of a given set of nodes? The answer is simply: turn on the Expression Plot checkbox as shown in above figure. Here is the pathway with this option is on:
The cursor and the value in the node represent the expression value of the current experiment (107th experiment). The size of the expression node can be changed, either by define the node size, or zoom in/out.
For the metanode, the expression plot is a recursive sum of its child nodes. The expression plot will only be shown if the metanode is contracted. If more than one child nodes have the expression profile, the average expression profile will be shown using the black-thick line. Following figure shows the expression plot of the above mentioned pathway (in the zoom-in state):
For the metanode, the cursor and value points to the average expression value.
Note: Similar to node label, the expression plot can also be turned on/off using individual control in the nodes menu:
The individual control of the expression plot is saved in the visML file.