Creating custom networks

Suppose that you're a horticulturist studying senescence and therefore interested in ethylene metabolism (alternatively: you're a student in the horticulture department at a university and your professor has given out an assignment to write a paper about the subject). You decide to start your search by looking for ethylene-related pathways in the world's most well characterized plant model organism: Arabidopsis thaliana.
In the top-right part of the MetNet Online website, a searchbox is always visible. You can use this searchbox to launch queries at anytime, from anywhere on the site. Given your interests, you type in ethene in the textbox, a common synonym for ethylene. Then, you click the Go button to launch the search.
The search result lists all compounds that have your search-string as part of their name, or at least on of their synonyms. As part of the results, you also find ethylene, your compound of interest. This means that MetNet Online is smart enough to figure out synonyms for compounds. Indeed, a search for H2O or water would have led your to the same compound, as well.
Once you click on the Ethylene/ethene compound, you're taken to the compound's detailed report. You see that the compound participates in three pathways. Note that in front of each pathway is a checkbox.
You don't really care about individual pathways. You just want to retrieve as much knowledge about ethelyne-related interactions as possible. You select all three checkboxes (or, by selecting the one checkbox in the header; which automatically selects or de-selects all pathways in the list). In the toolbar above the list you see a couple of icons. Clicking the first icon behind the word Visualize takes you to the visualition mode of MetNet Online, where you can get a graphical representation of the integrated result of the pathways that you just selected.
This is resulting representation for all three pathways in which ethelyne plays a role. The view is very much cluttered by transcription and translation events though. For your purposes, it would be useful to get a view of only metabolic and regulatory events. This can be done through the personalization features of MetNet Online. However, you will need to log into your My MetNet account first in order to access this functionality. So, click on the My MetNet button in the top toolbar.
If you weren't logged in yet, you're now presented with a login dialog such as shown here. You'll need your username and password. If you don't have a personal MetNet account yet, you can get one for free by following the instructions below the dialog box. Click the login button to continue.
This is the main page for the My MetNet personalization functions. Based on how much you've used your account, this may look slightly different on your screen. The basic build-up is always the same though: you can see some summarized profile information, see what you have bookmarked on the site thus far, and track your entity-lists (to learn more about lists, see our second use case).
The first thing that you want to do is bookmark the ethene entity. The easiest way is probably by re-doing the search. Yes, there's some repetitive work here, and as you become more familiar with our site, you may find yourself logging into the personalization framework automatically.
Once you're back on the entity's page, you'll now notice a big gold star in the top right corner (under the main menu bar). Click the star to add ethene to your bookmarks.
After clicking the button, you get an instantaneous confirmation that the entity was added to your bookmarks. Don't worry about accidentally adding something twice: in that case you get a message saying that the entity is already bookmarked. So go ahead and bookmark away!
Entities aren't the only thing that you can bookmark though. Your interest turns back to the pathways. While you hover over them, a thumbnail appears for each pathway. They look interesting, if only you could integrate them without the transcriptional en translational clutter (for your purposes this may be clutter, but it may be useful for somebody else. That's why the default pathway representation always contains as much information as we can muster).
Qs it turns out, there is a way that you can see partial pathways. You can bookmark any number of interactions from a variety of sources, and then ask to have them visualized together. To illustrate, click on the first pathway in the list. This brings up the details of the "ethylene synthesis and methionine cycle" pathway.
As you scroll down to the "Interactions" section of the page, you'll notice that you can select individual interactions and then perform different operations on them. You could select a number of interactions here and ask to have them visualized directly. However, for our purposes, we'd like to see an integrated set of interactions from different pathways. For now, there's no other way to do this then work through bookmarks. So, after selecting all interactions of this specific pathway, safe the transcription and translation events, select the bookmark button (big yellow star in the right of the toolbar).
After pressing the bookmark button, the system provides feedback and tells you which interactions were bookmarked. Don't worry about adding an interaction twice: the system is smart enough to figure out which ones you've added already and which ones you haven't. Each interaction can only be bookmarked once. The interface will actually tell you if an interaction has been bookmarked previously.
You want to combine interactions from all three pathways, so go back to the "ethylene" page (use your bookmarks for quick access), and select the second pathway in the list.
For "ethylene signaling", you follow the same procedure. Scroll down the page to get to the list of interactions.
You can skip right by the transcription and translation events...
... and select only the interactions of interest to you. In this case, we observe mostly signaling events that will nicely overlay with the metabolic mechanisms in the other pathways. After selection, add the interactions to your bookmarks.
A confirmation appears again, indicating which interactions were bookmarked.
Time to add the interactions of the third pathway. This is a regulatory pathway.
Scroll down to the interaction list and select your interactions of interest.
For the third time now, you receive confirmation that you bookmarked a set of interactions.
Now, let's see where all those bookmarks ended up.
By clicking on the "My MetNet" heading in the main menu bar at the top of your browser screen, you're taken your personalized MetNet portal. This page already tells you that you have 47 items bookmarked, and you can tell that at least some of them are interactions.
Click on the blue arrow next to the "Favorite bookmarks" heading for a detailed list of all your bookmarks.
As you scroll down the list, you can see that all of your bookmarked interactions are there. There's really only one thing left to do, and that's to look at the integrated result of all relevant interactions from all ethylene-related pathways. That's what the link "Visualize these interactions into a single network" does for you.
After clicking the link, you're taken back to MetNet's visual interface. It look very similar to when you visualized individual pathways earlier on, except this time there's no reference to individual pathways in the left panel. All you see are the combined bookmarked interactions.
Note the export toolbar that appears in the top-right corner of the screen. From here, you can take your network places. Both graphic formats (for publication purposes) and data-formats (for downstream processing in other applications, such as CytoScape or GraphViz) are supported.
This is what the Full ethylene network looks like, exported as a PNG file.

This concludes our tutorial on use case 1, which was an illustration of you can construct custom networks with the MetNet Online website. You can select another tutorial if you wish.

Copyright Wurtele lab