Structure & Workflow

PathAct view window is divided in different panels.

The upper bar (1) includes, from left to right:

• The Jobs button
• Settings button
• The user name, once you have already logged in.
• Profile, where you can change your profile information and settings.
• Logout, the logout button.
• Info, where you can find a link to the documentation of the tool.

• Back: Allows you to go back to the jobs view,where you can create new jobs or view existing jobs.
• Update: When genes are selected, it will update the pathways with the selected expression.
• Clear: Removes all genes and updates the pathways with the initial values.

The pathway viewer panel (3) shows the scaffold of the different signaling pathways supported by the web tool. Nodes are colored with a level of intensity proportional to their expression. You can navigate through the pathways by selecting the desired pathway in the Pathway list panel (4).

The pathway viewer is an interactive window where you can select any gene of a pathway by clicking on it. A window will appear showing the level of expression that the selected gene has in the current sample. This value can be modified as desired inside the range [0,1].

The pathway viewer also shows the result of the experiment performed, by coloring the significant circuits in different colors. For further information in the interpretation of the results, see Results.

The pathway list panel (4) lists all the available pathways. You can visualize a particular pathway into the Pathway viewer panel (3) by clicking on the corresponding name into the pathway list.

The circuit list panel (5) lists all the available circuits included in the current pathway selected in the pathway list (4).

You can select any of these circuits in order to make it stand out among the others. By clicking again on the name of the selected circuit, all circuits will be highlighted again.

The Add genes panel includes the Search genes window and the list of genes with modified expression.

• Update: Each time you press the button Update, a comparison between the signaling values of the pathways in the current sample and the signaling values resulting from the modification of the expression values in the current sample by the selected values is performed. The results of this comparison can be visualized in the Pathway viewer panel (see Results) and by pressing the Show last update report button.
• Search genes: You can also search the desired genes to be modified in this window.
• Modified genes list: List of the genes whose expression has been modified, together with the new value of their expression. In order to remove a gene from the list, press the x button next to its expression.

The related drug list panel (7) lists the drugs including as target any of the genes selected in Add genes (6). You can simulate the application of any of this drugs by checking their corresponding checkbox.

The add drugs panel (8) allows to search and add drugs directly.

The genes affected by drugs (9) lists the genes whose expression is being modified by any of the selected drugs in the gene related drugs panel (7).

Further information on the kind of drug is also displayed in the list.

The Show last update report button shows a new window with the report of the results for the current comparison. This report includes two fields:

• Input: Lists the genes whose expression has been modified in the current comparison, and the new expression value.
• Path impact: Lists the names of the pathways, ordered by the absolute value of their fold change (also log(Fold_Change)). An absolute fold change greater than 2 is considered significant. Therefore, an absolute log fold change greater than log(2)= 0.6931472 is significant.

In order to close this window and return to the tool page, you can press the x button on the right upper side of the window.

In this window you can configure the fold change threshold beyond a circuit is considered statistically significant.

Also can configure the effect of each type of drug by clicking on the Settings button.

This panel shows the last update gene list with it's activity status. Last update gene list