Quick tour of Narada:

1. Load files.

   
   1. Load Network Files

      Network files need to be of simple interaction file format (SIF). For gene regulatory networks, the interactions are directed, so the order in which the genes is specified is important. The mode of interaction is specified using ``(ur)'', ``(dr)'' and ``(ud)'' for up, down and dual-regulation respectively. For PPI networks, the edges are undirected and mode of interaction is specified using ``(pp)''.

      Interaction files should use gene names or uniprot protein names.

      You can load multiple network files, they will all be listed in the left column. For networks with less than 1000 nodes a view will automatically be created. Right click on the name to create/remove view and remove network.

   2. Load Gene Ontology + Gene Annotation Files

      Gene Ontology file must be in obo format. Annotation files need to be in goa format. Multiple files can be added (for different species).

2. Network Layout

   

   To change layout for currently viewed network

3. Narada plugin menu:

   
   1. Color Graph

      To change visualization style. Toggle node names (Gene ontology term id and name)

      
   2. Annotation
      

      Select (bp, mf, cc) annotation based on level. Select terms using 'Ctrl'+ for terms to short-circuit. Children of selected terms will be removed from the annotation.

   3. Search Pathways (Forward/Reverse Searches) :
      

      1. Select term for pathways (starting or ending point) or find paths for all terms (bulk processing ... takes long time).

      2. Select direction: Forward (paths regulated by term) or Reverse (paths regulating term)

      3. Extend all paths (significance computed only at leaf) or only significant paths (significance computed at each intermediate node).

      4. Max length: search paths with at most X edges.

      5. Select alpha value. Paths with p-value less than this are displayed.

   4. Search for GO Path :
      

      Select GO terms (GO:00XXXXX) and edge attributes between nodes, if any such paths are found in the current network, they will be displayed along with significance of path

   5. GO Tree Graph :
      

      Result of reverse search pathways (for DNA repair). Leaf nodes have popup menu: (a) linkout to web services. (b) Highlight path in gene network as shown below. (c) Open a new GO path (next section). (d) Properties showing freq and p-value.

      
   6. GO Path Graph :
      

      Single GO path, allows to move up/down the GO hierarchy at each node. Background menu offer to highlight path and show freq and p-value.