PathAct view window is divided in different panels.

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

• The home 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.

This button allows you to go back to start page, where you can create new jobs or view existing jobs.

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 gene list panel includes the Update button, the Search genes window an 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 Additional drug targets list (7) lists the genes whose expression is being modified by any of the selected drugs in the Related drug list panel (8).

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

The related drug list panel (8) lists the drugs including as target any of the genes selected in Gene list (6). You can simulate the application of any of this drugs by checking their corresponding checkbox.

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.

In the expression matrix panel (2) you can upload the expression matrix you are interested in working with. Only the first column of the data matrix will be considered.

You can load different files to work with, and all of them will be listed in the panel, allowing you to use equally one or another. Files can be loaded as:

• Load example file: An example data set will be loaded, consisting in a unique sample of a Breast Cancer cohort taken from The Cancer Genome Atlas repository.
• Load file: Allows you to upload a file from your computer. The data is arranged in folders as in a personal computer. You can upload data to any folder and organize it as desired. For further information on how to update data to PathAct, see Upload your data.