Searching

MetNet Online contains hundreds of pathways, thousands of interactions and tens of thousands of entities. Certainly you wouldn't want to explore them one by one. And in many cases, you don't want to do any exploring at all: You have a gene or a metabolite and you need information... now!
At any given time, there's a textbox in the top right corner of the screen that allows you to search for anything that you're interested in. Let's say that we're searching for glucose.
After submission, we find quite a few hits. In order to let you quickly navigate to where you want to be, results are grouped by type. Entities (and their synonyms) are searched, as well as pathways. You'll find a great many proteins e.g., since many enzymes interact with glucose in one way or another.
If we're looking for the hexose, we need to expand the "metabolite" branch. Entities that have "glucose" directly in their name, are displayed first (alphabetacally). Further down, you find entities that don't match right away, but the word "glucose" appears as part of one of the synonyms for the entity (this is especially relevant for genes and proteins, which have their systematic name assigned as a default title).
α-D-glucose is one of the more common forms of glucose in living organisms. When we select it from the list, the details for the entity appear. The entity is in three pathways.
If you don't want to examine each pathway individually, you can select all three pathways together.
You can see an integrated network and visualize all selected pathways in a single view by clicking the icon.
The integrated network is usually large and may take a while to load initially (after which it is cached, you it will load quicker if you request it again). The interface to browse the integrated network is the same as the one you use to browse individual pathways.
Seeing what pathways are linked to a single entity is not always what you want! Sometimes you have a list of genes or metabolites that you want to give meaning to.
A Fisher exact test over all relevant pathways can be useful. That's what the "Common pathway" menu option gives access to on the search menubar.
Here you can enter a list of either genes or metabolites. In order to just try it out, you can select the list of genes from the right of the screen and copy them into the textarea.
Make sure that you specify whether you're entering metabolites or genes, and select what organism you target.
Running the search will result in a list of pathways in which your entities participate, ranked by most likely relevance. You can read more about how the p-values are calculated elsewhere on the site.

This concludes our tutorial on how to search the MetNet Online website. You can select another tutorial if you wish.


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