PathArt Quick Start Guide

   Download Tutorial (MS Word)

This guide is intended for users that have a predetermined list of “interesting” genes which they are interested in mapping to pathways.

PathArt currently has information from Human, Mouse, Rat pathways. Some pathway components may have no information associated with them.

To begin, make sure that your list of genes consists of Affymetrix, Agilent, GenBank, LocusLink, UniGene, or HUGO ID’s. This list may be in any format as long as it is able to be pasted in column format with one gene ID per line. Select all the genes you are interested in examining and copy them to the clipboard.

Start the PathArt application and select Component from the Search menu.

Alternatively you can select Component Search from the Toolbar.

You will now see the following window:

Click the Public Domain radio button and click inside the window below so that a cursor becomes visible. Use Ctrl-V to paste your gene list. Select the proper ID type from the drop-down menu. If you are using HUGO ID’s, select GeneName. Once this is done, click View Pathways.

Viewing Pathways

After clicking the View Pathways button, you will see the following window:

The left window displays every pathway that includes one or more of the genes you imported. The right window shows a hierarchical listing of the genes included in the pathways outlined in the left window organized by organism, physiology/disease, and pathway. To view interactions within a pathway, click on the pathway of interest in the left window.

Clicking on a pathway will bring up the following window:

The pathway diagram on the right consists of boxes that represent pathway components and lines and arrows that represent interactions. Click on the Legends tab to see what each shape and line represents (see below).

If you click on any component in the pathway diagram, you will see the annotation for that component appear at the bottom in a new window. Pictured below is the PathArt database entry for a gene. It should be noted that not all components shown in every pathway may be annotated.

This panel includes three different tabs: Function, Sequence, and Localization. The Function tab includes brief descriptions of the gene’s function as well as links to the references that describe the function. The sequence tab provides chromosome and band information as well as links to GenBank and SwissProt. The Localization tab provides a list of the tissues in which the currently selected gene is expressed.

If a line or arrow describing an interaction between components is selected the following window is seen replacing the above window:

This panel includes two different tabs. The Description tab describes the type of interaction and the method by which the interaction was detected. A link to the original paper describing the interaction is also included. The Localization tab describes the organism and cell type from which the components used in the discovery of the interaction were derived.

Exporting Information From PathArt

You have the option of exporting a variety of result types from PathArt. This section outlines how to export the more widely used results.

To save an image of the pathway diagram:

Once you have loaded the pathway you are interested in, you have the option of exporting a jpeg image of it. Make sure that you are viewing the very top left corner of the pathway diagram as in the picture below:

Note that the horizontal scroll bar is all the way to the left and the vertical scroll bar is all the way to the top. If you attempt to export an image from any other position, part of the pathway diagram will be clipped.

From the File menu, select Save. Click Graph… in the subsequent menu.

You will now see a save file dialogue:

Give the file a meaningful name, select the location where you want it saved, and click Save. You will now be able to open the pathway diagram in any image viewer or import it into PowerPoint or Microsoft Word.

To export annotation information:

There is no formal tool to export pathway component or interaction annotation, but it can easily be copied and pasted into Microsoft Word. Begin by selecting the component or interaction that you are interested in.

Select the tab in the annotation window that you want to export and click within the window. Use Ctrl-A to select all of the text in the window.

Press Ctrl-C to copy the text and then paste it into Microsoft Word or another text editor.

Alternatively, if one is interested in exporting all interactions or components from a selected pathway, generate a Report containing the elements you are interested in from the left window by selecting the Report tab and clicking the desired elements and clicking the “Apply” button. When the Report is generated, follow the above instructions to Select, Copy and Paste the Report.

This concludes the PathArt Quick Start Guide. For more detailed information, please see the PathArt Tutorial or the PathArt User Guide.