PathInsight is an open-source Cytoscape application created to aid in modeling the upstream and downstream signaling effects of small molecule binders in a biological pathway. Users may perturb a given system through a series of steps and observe the affected pathway under various pre-defined conditions. PathInsight also allows for the use of visualization in Systems Biology Graphical Notation.
PathInsight is developed and maintained by Aarya Venkat (email@example.com) of the Gilson Lab (gilson.ucsd.edu) at UCSD.
Installation (Two Methods)
1. Either download from http://apps.cytoscape.org/apps/pathinsight 2. Or open Cytoscape. Click on Apps > App Manager > PathInsight Download the sample network from: https://github.com/HelloAarya/PathInsight/blob/master/jakstatsbgn.cys
PathInsight functions are located in Cytoscape under Apps > PathInsight
- Node Analysis: An algorithmic analysis that models how a selected activated or inactivated node (or nodes) will affect their nearest neighbors. May be performed in one step (nearest neighbors) or two steps (nearest neighbors + neighbors of nearest neighbors) or N-steps (recursive algorithm that operates the number of times a user specifies).
- Activated – Gives selected nodes a value of one.
- Inhibited – Gives selected nodes a value of negative one.
- Reset – Gives selected nodes a value of zero.
- Activating – Gives selected edges a value of one.
- Inhibiting – Gives selected edges a value of negative one.
- Reset – Gives selected edges a value of zero.
- Reset Nodes – Resets all node values to zero.
- Reset Edges – Resets all edge values to zero.
- Clear Images – Erases all painted images.
- Clear Questions - Erases all question marks from edges.
- This purely visual feature takes any edge that has previously been allocated a value of activating (+1), inhibiting (-1), or null (0) and gives it a corresponding circle, T, or diamond interaction symbol. Furthermore, if the pathway is taken directly from a KEGG source (like KEGGScape), edges are automatically changed based on provided information.
- This function also gives any node labeled with an integer value, previously set by Node Analysis or Node Label tabs, a corresponding image of the value. Users may use this to visually model the effects of a perturbed pathway.
- Phosphorylated -- visual function adding a yellow dashed line to an edge specified as phosphorylating.
- Dephosphorylated -- visual function adding a pink dashed line to an edge specified as dephosphorylating.
SBGN (Systems Biology Graphical Notation)
- Draw Chemical Node -- creates a circle shape (or replaces a node with one if a node is selected)
- Draw Macromolecule -- Replaces a node with the SBGN value for a macromolecule
- Draw Gene -- Replaces a node with the SBGN value for a gene
- Draw Process Nodes -- Creates a node that represents translocation or dimerization
- Draw AND Gate -- Creates a node that represents an AND gate
- Draw OR Gate -- Creates a node that represents an OR gate