NeAT - Pathfinder

Do multiple-to-multiple end path finding. Click on help for help.
Web service and interface by Karoline Faust. This program calls REA (Jimenez and Marzal, 1999). See Credits for other contributors.

1. Network help



The network has been already uploaded. Its network identifier is: Pathfinder_tmpGraph_d597cd86-3095-475f-99e7-d70a542d072a.tab

Comment on the demonstration example

In this demo, the network has been already pre-loaded. We use the weighted STRING database network, a network of protein-protein interactions, as demo network. Its weights, which describe edge reliability, have been inverted to describe edge costs. The demo network is part of our sample data collection. We want to recover a signal transduction pathway known to regulate cell wall integrity in S. cerevisiae (Saito and Tatebayashi, J. Biochem, 2004). This pathway is reported to start with WSC1 or MID2 and to end with RLM1, SWI4 or SWI6. We will look for the lightest paths connecting MID2 to RLM1/SWI4/SWI6, WSC1 being absent in the demo network. The paths of first rank miss one step (ROM2) and replace MPK1 by KSS1, otherwise they are correct. ROM2 is missing in the demo network. With improved quality of the protein-protein interaction network used, path finding accuracy is expected to increase.


2. Seed nodes help



Info: Matching of provided identifiers to identifiers of nodes in the network is case-insensitive.

Enter source and target nodes:

Source nodes  
Target nodes

Or upload a batch file:



3. Path finding options help



The weights have been already set.
Rank
Identifiers of nodes to exclude
Identifiers of nodes to include
Maximal path weight
Maximal path length
Minimal path length



4. Output help



Output format  

Table:
Graph:
       Graph format:       
       Graph output type:


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