PNmerger: a Cytoscape plugin to merge biological pathways and protein interaction networks http://www.hupo.org.cn/pnmerger Fuchu He E-mail: hefc@nic.bmi.ac.cn Tel: 86-10-68171208 FAX: 86-10-68214653 Yunping Zhu E-mail: zhuyp@hupo.org.cn Tel: 86-10-80705999 FAX: 86-10-80705155 2008-8-28
Contents 1 Overview 2 Download and Installation 3 Control options 4 Result display 5 Result tables 6 Visulization of selected pathways and crosstalk elements in Cytoscape 7 References 1
1. Overview PNmerger(a biological Pathway and protein Network merger) is a java based plug-in for the widely used open source Cytoscape molecular interaction viewer. Cytoscape is a bioinformatics software platform for visualizing molecular interaction networks and integrating these interactions with gene expression profiles and other state data. PNmerger integrates KEGG pathway information into Cytoscape. Given an input interaction network of certain organism, PNmerger can present known interactions, potential protein-protein interactions, crosstalk proteins and crosstalk interactions in the input network. Users can view PNmerger results in Cytoscape output panel. 2. Download and Installation Before installing the PNmerger plugin, you must have Cytoscape installed on your computer. Please download the latest version of Cytoscape from the Cytoscape project website http://www.cytoscape.org/ and download both PNmerger.jar and prefuse.jar from PNmerger website http://www.hupo.org.cn/pnmerger. Please place them into the local Cytoscape/plugins directory. Start Cytoscape. If PNmerger installation is successful, you will see that PNmerger appears in the Plugins menu of Cytoscape (Fig 1). If it does not, you maybe place the jar files in the wrong directory or your java environment is lower than Java SE 6.0. After verifying that you have placed the two jar files into the correct directory, please restart Cytoscape to reload the plugin. Fig. 1. Position of the PNmerger plug in in Cytoscape 3. Control options When Cytoscape is started, click the PNmerger from the Cytoscape plugins menu (Fig 2) to show the control panel of PNmerger. There are two options on PNmerger control panel (Fig 3). 2
Step 1: select the organism of the input interaction network. Now, the version 1.0 of PNmerger supports Homo sapiens (human), Saccharomyces cerevisiae, Caenorhabditis elegans(nematode), Drosophila melanogaster(fruit fly), Mus musculus(mouse) and Rattus norvegicus(rat). Notice: PNmerger 1.0 only supports gene name and protein name format inputs. Step 2: select the pathway category: signal transduction pathways/ metabolism pathways/ regulatory pathways. Step 3: click Analyze button. Fig. 2. How to start PNmerger 3
Fig. 3. PNmerger control panel 4. Results display PNmerger adds pathway information as an attribute of each node in the input network. If certain node in the input network appears in more than one pathway, PNmerger adds several copies of the node into the input network. If certain node appears in k pathways, PNmerger adds k-1 copies of that node; each copy has the same attributes as the original node except the pathway attribute. For instance, node A appears in pathway X, pathway Y and pathway Z, PNmerger sets pathway X as the pathway attribute, then adds two nodes A(copy1) and A(copy2) with pathway Y and pathway Z as their pathway attribute to the input network. If certain node in the input network does not appear in any pathway, PNmerger sets unsigned_class as the pathway attribute for it. Also PNmerger adds crosstalk protein information as a node attribute to judge whether the node is 4
a crosstalk protein. Integrating another Cytoscape plugin Cerebral, PNmerger can layout network according to the pathway attribute of each node. PNmerger can also display crosstalk proteins using an eye-catching color which is different from other nodes. Fig. 4. PNmerger result display Fig. 5. PNmerger result display for crosstalk proteins 5
5. Result tables PNmerger result panel contains four tables. The users can click the title of certain table to expand it. The Crosstalk Proteins in Network table shows crosstalk proteins that are found by PNmerger in the input network. Column 1 displays the name of crosstalk proteins; column 2 and column 3 represent the other two proteins which connect corresponding crosstalk proteins. Column 2 and column 3 provide the pathway information of the two proteins. The Crosstalk Interactions in Network table shows crosstalk interactions that are found by PNmerger in the input network. Column 1 displays the two proteins names of each crosstalk interaction. Column 2 and column 3 provide the pathway information of the two proteins. The Known Interactions in pathways table shows known interactions found by PNmerger. These interactions are found both in input network and KEGG pathways. Column 1 and column 2 are the two proteins names. Column 3 is the pathway information of the interaction. The Potential PPIs in Pathways table shows potential protein-protein interactions that are found by PNmerger. These interactions are present in the input network and absent from the pathway interactions. Column 1 and column 2 are two proteins names. Column 3 is the pathway information of the interaction. Fig. 6. PNmerger result tables. 6
6. Viewing selected pathways and crosstalk elements in Cytoscape The users can focus on certain crosstalk elements in Cytoscape. Fig. 7. Focus on a certain crosstalk protein. Fig. 8. Focus on a certain crosstalk interaction. By extracting the information of KGML format pathways, we convert them to the GML (Graph Markup Language, http://schemas.stylusstudio.com/graphml/index.html) format. Our result can be visualized in Cytoscape perfectly. Select a row in the last two tables, then click View selecting pathway, the users can view corresponding pathway in Cytoscape. All pathways are saved as GML format in our plugin. With this function, the users can see analysis result of PNmerger smoothly and clearly, and get something which they are interested in. 7
Fig. 9. View a known interaction in certain pathway. Fig 10. View a potential protein-protein interaction in certain pathway. Also the users can export certain table to a text file. 7 References 1 Suderman M, Hallett M. Tools for visually exploring biological networks. Bioinformatics, 2007, 23(20): 2651-2659 2 Shannon P, Markiel A, Ozier O, et al. Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks. Genome Res., 2003, 13(11): 2498-2504 3 Maere S, Heymans K, Kuiper M. BiNGO: a Cytoscape plugin to assess overrepresentation of Gene Ontology categories in Biological Networks. Bioinformatics, 2005, 21(16): 3448-3449 4 Avila-Campillo I, Drew K, Lin J, et al. BioNetBuilder: automatic integration of biological networks. Bioinformatics, 2007, 23(3): 392-393 5 Barsky A, Gardy J L, Hancock R E W, et al. Cerebral: a Cytoscape plugin for layout of and interaction with biological networks using subcellular localization annotation. Bioinformatics, 8
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