1. Lions and Tigers and Bears, Oh My!
SFLDLoader
Lions and Tigers and Bears, Oh My!
Structures
Groups
and batchTool, too!
John "Scooter" Morris, Ph.D. UCSF
Cytoscape Developers Retreat

2. Protein Similarity Networks
Complex networks
Nodes = proteins
Edges = measure of sequence similarity
BLAST e-value
Research goals:
Understand relationships between groups of proteins (families)
Gives clues to function
Understand relationships between a protein and groups of proteins
Search for linkers (evolutionarily important proteins)
Search for representative proteins

3. Protein Similarity Networks

4. SFLDLoader Interface to the Structure-Function Linkage Database
SFLD is a deeply curated database of protein superfamilies
SFLD exports superfamilies, subgroups, and families to XGMML
SFLDLoader provides a way to browse SFLD and load networks

5. SFLD Loader Bring up SFLDLoader
Select amidohydrolate->phosphotriesterase
Load

6. SFLDLoader Future directions: Allow selection of cut-off values
Significantly reduces size of network
Allow selection of attributes
Reduces size of XGMML download
Allow selection of groups of families & subgroups
Provide a search interface
Resulting network will locate protein of interest within the network

7. Groups Lots of families and subgroups
Named selections make finding them easier
Creating metanodes and significantly improve visualization of linkers and unknowns
Plugins:
groupTool
Interface to low-level CyGroup mechanism
namedSelectionPlugin
JTree interface to groups. Supports concept of “remembered” selections
metaNodePlugin
Supports concept of expand/contract

8. Groups Bring up Amidohydrolase
Create a named selection (phosphotriesterase)
Browse namedSelection
Show selection, cleared selection
Create a named selection (PTE)
Show how remembered selection works with both
Use groupTool to create groups for all subgroups (make them metaNodes)
Show collapse all
Expand phosphotriesterase
Expand phosphotriesterase-like

9. Groups Future directions: (many) more viewers
easy to get metaNodes confused
overlapping membership is a hard problem
undo/redo support
group creation
node/edge addition/removal
viewer-specific (e.g. expand/contract)

10. structureViz Understanding structure helps us understand function
structureViz provides a link between Cytoscape and UCSF Chimera
Can be used to:
visualize protein structure
compare structures
map structural metrics back to Cytoscape
detect clashes

11. structureViz

12. structureViz Future directions Allow searching of ModBASE
modeled structures
Integration with PiBASE
database of domain-domain interfaces
Clash detection

13. batchTool
Users wanted to output many (100’s) of networks at different cutoffs/different data
Very laborious problem
batchTool provides a simple command execution capability

14. batchTool batchTool commands: open sessionfile
Open a session file
import [network|node attributes|edge attribute] filename
Import a network or attribute data
layout layout-algorithm tunable1=value1 tunable2=value2 etc.
Layout the network using the layout layout-algorithm with the tunables set to the appropriate values
export [vizmap|node attributes|edge attributes] to filename
Export the vizmap and node or edge attributes to a file
export network as [XGMML, PSI-MI, GML, SIF, PDF, SVG, PNG, GIF, JPG] to filename
Export a network as either a network data file or a graphics file

15. batchTool batchTool commands (cont); save as filename apply vizmap
Save a cytoscape session
apply vizmap
Apply vizmap map vizmap to the current network
exit
Exit cytoscape

16. Example test.com cytoscape.sh -S test.com import network pte.xgmml
import node attributes subgroup.noa
layout force-directed
export network as pdf to test.pdf zoom=10
Exit
cytoscape.sh -S test.com

17. Example

18. Summary Using Cytoscape and plugins we can:
provide valuable tools for the study of protein function
use these tools to understand protein relationships
understanding these protein relationships can give us clues about protein function and evolution
this can help us with hypothesis formation and selection of “interesting” proteins to study in more depth

19. Acknowledgements Ferrin Lab Cytoscape Consortium Agilent Technologies
Conrad Huang
Elaine Meng
Leonard Apeltsin
Tom Ferrin
Cytoscape Consortium
Mike Smoot
Agilent Technologies
Allan Kuchinsky
Babbitt Lab
Scott Pegg
Holly Atkinson
Shoshana Brown
Patsy Babbitt
Conklin lab
Alex Pico
Funding
NIH National Center for Research Resources (grant P41-RR01081).

20. Thanks!
Questions