PathArt Basics Tutorial

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Once you have started the PathArt application, you have three choices of how to proceed. You may begin by searching the PathArt database based on a specific gene, based on a particular pathway, or by importing microarray data.

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

Searching by Specific Gene

First, select Component from the Search menu.

Alternatively you can select Component Search from the Toolbar.

You will now see the following window:

You may either search the list to the left of the window and select the genes you are interested in, or type or paste a list of genes in the box located on the right-hand side of the window. If you are typing a list, you may use Affymetrix, Agilent, GenBank, LocusLink, or UniGene ID’s. In addition, you may also type in the gene name (HUGO). Be sure to set the ID Type selector to match the ID type you are using.

Once you are finished either selecting or typing your set of genes, you may click View Report to see more information about each gene, or View Pathways to see the pathways that your genes are involved in. Below, an example of a report is shown. For more information about the pathways output, see the Viewing Pathways section.

Example of Report Window  

Searching by Pathway

Begin by selecting Pathway from the Search menu.

You will see the following window:

You can filter the list of pathways by selecting either a particular organism, disease, physiology, or a combination of all three. Once you have found the pathway that you are interested in, select it and click the View Pathways button. For information regarding viewing pathways, skip ahead to the Viewing Pathways section.

Searching based on Microarray Data

First you will need to prepare your data so that PathArt will recognize it. Your data must be separated by tabs or other delimiters into columns. PathArt will accept the following column configurations:

			  Gene Identifier	 	Expression Ratio
              Gene Identifier 		Cy3 Cy5
              Gene Identifier 		Cy3 Cy5 Expression Ratio
              Gene Identifier 		Expression Ratio 1 Expression Ratio 2 …

Once your data is properly formatted, click the multi-colored square icon in the top left corner of the window:

This will bring up the open file window below. Navigate to your formatted microarray data, select it, and click Open.

You will now see a window that allows you to specify the column configuration, delimiter, and gene identifier type. Set all these to the proper values and click OK.

You will see the following window:

You may click View Report to see information about the genes contained in the file you just imported, or click View Pathways to map the genes onto the relevant pathways. An example of the report is pictured below. For information regarding viewing pathways, skip ahead to the Viewing Pathways section. You may also set the Matrix or Linkage options, but do not rely on PathArt for your statistical analyses or normalizations which should be performed in an appropriate microarray analysis software package prior to importing the data into PathArt. PathArt is a tool for viewing interactions between genes.

Viewing Pathways

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

The left window displays every pathway, disease, and organism that includes one or more of the genes you selected. Alternatively, if you selected a specific physiology or disease, every pathway for all organisms annotated to include that physiology or disease would be displayed. 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. If you imported microarray data, the genes represented in that array will be colored based on their expression level (green for high expression and red for low). 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 of the 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.

If one wants instead to view annotation of all components of a given pathway, click on the Results tab in the left window. One can select from the menu within this window features of the various pathway components. Once the desired components are selected hit the Apply button to generate a Report. A window showing a Report selected for Sequence, Location and Function is shown below. Note that you may have to scroll down within the Report window (right) to view Report contents as it may initially appear blank.

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 other word processing program.

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 Tutorial. For more detailed information, please see the PathArt User Guide.