John 'Scooter' Morris

University of California, San Francisco

Biological Use Case: Find possible complexes, protein families, functional relationships and view in biological context.


Cytoscape version: Version number (2.6)

Plugins to Load: ClusterMaker (from what URL?)

GUI steps:

Describe each step (story), the GUI action to take, and probable remarks




Start with expression data for studies into mechanism for galactose utilization.

open galfiltered.cys session

galfiltered may be replaced by time series data from Nathan Salomonis, AllanK will follow up on this

run clustering to determine interesting subnets

select plugins -> cluster -> hierarchical cluster. For settings, use maximal linkage, cluster attributes as well as nodes, cluster on just expression data

visualize and navigate the clusters

on treeview window, explore by clicking on points on the dendogram. Press 'map colors onto network' diagram

shows Eisen treeview visualization. Clicking/selecting a particular row in the heatmap will result in the expression values for that column being overlaid on the network view

adjust contrast by settings -> contrast

use shift-drag to draw a box and see results on network

use shift-click to pick individual columns

select an individual row by clicking on it

animate expression values over time

select 'options'. On popup, click on specific attributes to select. Optionally order attributes. Select all attributes and click on 'animate'.

will show nicely if we have time series data. TODO: AllanK check with Nathan on this

Data Files: Attach data files

Presentation: Attach your presentation

Webstart: Attach a webstart

Video: Attach a video link

ClusterMakerRecipe (last edited 2009-02-12 01:03:02 by localhost)

Funding for Cytoscape is provided by a federal grant from the U.S. National Institute of General Medical Sciences (NIGMS) of the Na tional Institutes of Health (NIH) under award number GM070743-01. Corporate funding is provided through a contract from Unilever PLC.

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