This tutorial consists in a quick start to ChalmyNET. Next we briefly introduce the basic functionality of ChlamyNET. For more details, please take a look at our case studies or check this video tutorial.
1. Getting familiar with the interface
ChlamyNET is visualised using a customisation of the software tool WiGis. Our interface is composed of the following interactive panels:
2. Exploring the gene co-expression network
IMPORTANT: ChlamyNET shows the results in a separate window. In order, to be able to open this window it is necessary to allow ChlamyNET to open pop-up windows.
A single gene can be selected in ChlamyNET by either clicking on the corresponding node in the Detail view or by using the Search panel. Once a single gene has been selected, the Selected Locus Detail interactive panel shows some relevant topological information such as the clustering coefficient, hub score, PFAM annotation and degree, see (1) in Figure 2. Additionally, the Analysis section on the Selected Locus Detail can be used to identify transcription factor binding sites (TFBS) on its promoter (see (2) in Figure 2), visualise the annotation of its neighbour genes (see (3) in Figure 2), represent its expression profile and that of its neighbours using line and heatmap graphs (see (4) in Figure 2), determine significantly Gene Ontology (GO) terms in its neighbour genes (see (5) in Figure 2) and identify significant TFBS on the promoters of its neighbourhood (see (6) in Figure 2).
Sets of interesting genes rather than indivual genes can also be studied using ChlamyNET. These genes can be identified by typing in the Search panel either their identifiers or PFAM annotation. Once the genes have been found they can be selected one by one by click on the boxes preceding their identifiers or all of them can be selected by clicking on Select all. Note that on the Overview panel the selected genes are highlighted in red. In the following subsections we describe how to perform relevant analysis over selected gene sets using the Analysis section on the Search interactive panel.
3. Customising the apperance of nodes, edges and labels
Our gene co-expression network is very large and some regions are very crowded with nodes and edges. The overlapping of nodes, labels and edges makes difficult to visualize these regions using the default settings. This problem can be alliviated by manually tuning the general visualization parameters from the Apperance panel, see Figure 4. The width and height of the entire interface can be changed using the slides in the Apperance panel. Using this panel the node size, edge thickness and edge color can be tuned as well. If you are not interested in highlighting the neighbours of a selected gene you can uncheck the corresponding box in the Apperance panel.
Visualization parameters for the labels associated with genes can be tuned using the interactive panel Labels, see Figure 5. Most of these parameters are self-explanatory. For example, if you want to hide all the labels you will need to uncheck the Show labels box.
4. Troubleshooting: system requirements and browser compatibility
In order to visualise our gene co-expression network, you will need a recent Linux, Windows or Mac operating system with a recent version of Java installed and enabled in your web-browser. Currently, WiGis only fully supports the web-browser Firefox. You can download it from here.
Please note that our gene co-expression network is very large and loading it can take more than a minute, especially when you access it for the first time from your computer. Beware that sometimes your web-browser might load the previous visualization of the network from its cache. In order to solve this just reload the page by, for example, pressing the F5 button.
Should you experience any problems when visualising, exploring or customising our gene co-expression network, please send an email to us.