PathInsight

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 (aarya@ucsd.edu) 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

Function Guide:

• 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).

• Node Label:

  • 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.

• Edge Label:

  • 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 Values:

  • 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.

• KEGG Prepare:

  • 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.

• Phosphorylation

  • 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

Example