Tutorial

Download the sample tryptophane synthetase data and load it into Medusa using

File->New. Select Display ->Interactions (or alt-d alt-i). Change the Display -> Alpha conf

setting to show edges as dashed lines (solid line is highest confidence followed by dense

and sparse dashed lines).

Suppose we have determined a link between SYW_PROMA (Tryptophanyl-tRNA

synthetase (EC 6.1.1.2) (Tryptophan--tRNA ligase) (TrpRS) in Prochlorococcus marinus;

see STRING) and TRPA_THETN (TRPA in Thermoanaerobacter tengcongensis). Let's

call this evidence type 'experiments'. Right-press on one of these nodes and create a link

to the other by dragging the mouse to the other node. When you release, a dialog will

open. Choose 'experiments' from interaction type. Also, change color and shape by right-

clicking on the nodes

Let's remove some stuff we don't need.

First, remove the clusters of TRP genes that we are not interested in.

It is enough to select the hub nodes (selected in picture).

Choose "Manipulate -> Delete nodes".

All unlinked nodes are automatically removed, resulting inthe deletion of all TRP nodes

that are not linked to any external node.

Deletion can also be done by right-clicking on individual nodes

Use 'relax' to fix the layout

We saw no links corroborating the 'experiments' edge between our two selected nodes.

Let us see if we can find links in deeper searches.

First, remove the cox genes.

Then select the two hub genes and then select "Select -> Invert".

Now, all the fringe nodes should be selected.

Let's make a huge graph.

This graph is not very informative.

Deselect all nodes and select "Spring" from the bottom panel.

It may take some time to complete the layout. It should look something like in the image

Where are our nodes?

When we have many nodes, it may be difficult to find certain nodes.

Use the "Select -> by name" function and enter 'proma'