When Cytoscape has started, select PNmerger from the Cytoscape plugins menu to show the control panel of PNmerger. There are two options on PNmerger control panel.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).Step 2-select the pathway category: signal transduction pathways/ metabolism pathways/ regulatory pathways. Step 3, click Analyze button. With analyze result, PNmerger add 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 add several copies of the node to the input network. If certain node appears in k pathways, PNmerger add k-1 copies of that node, each copies is the same with the original node except the pathway attribute. For instance, node A appears in pathway X, pathway Y and pathway Z, PNmerger set pathway X as the pathway attribute, then add 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 set unsigned_class as the pathway attribute of it. Also PNmerger add crosstalk information as a node attribute to identify weather certain node is a crosstalk molecule. Integrated another Cytoscape plugin PNmerger, PNmerger can layout network according to the pathway attribute of each nodes. PNmerger can also show crosstalk nodes as an eye-catching color different with other nodes.