tYNA
Supplementary web site for

Kevin Y. Yip, Haiyuan Yu, Philip M. Kim, Martin Schultz and Mark Gerstein,

The tYNA Platform for Comparative Interactomics: A Web Tool for Managing, Comparing and Mining Multiple Networks

Go to the tYNA web site.
Supplementary Figures (please view the JPG files at 100% zoom level for best image quality)
Figure S1: Networks uploaded and categorized in the tYNA database.
Figure S2: Visualizing a network in a workspace.
Figure S3: Controls for image export and SVG viewer tips.
Figure S4: Single network operations (left) and network transfer options (right).
Figure S5: All cycles that involve three or more proteins identified from a regulatory network.
Figure S6: Multiple network operations.
Figure S7: Plugin for Cytoscape.
A PDF fle containing all the supplementary figures.
 
Supplementary Tables
Table S1: A comparison of several network analysis and visualization systems
  Cytoscape(2.3.1) JUNG
(1.0)
N-Browse
(10 Aug 2006)
Osprey
(1.2)
tYNA
(10 Aug 2006)
Basic NetworkAnalyzer plugin (1.0) Metabolica plugin (1.0)
Main purpose Visualization Network analysis Motif finding Graph library Visualization Visualization Network analysis
System Standalone Plugin Plugin Standalone Web Standalone Web
  • Link from external resources
Indirect: Java Web Start N/A N/A No Direct No Direct
  • Web service interface
No No No No No No Yes: SOAP
Statistics calculation No Yes No Yes No No Yes
  • Degree
No Yes No Yes No No Yes
  • Clustering coefficient
No Yes No Yes No No Yes
  • Shortest path length (eccentricity)
No Yes No Yes No No Yes
  • Betweenness
No No No No No No Yes
Motif finding No No Yes No No No Yes
  • Chain
No No No No No No Yes
  • Cycle
No No Yes No No No Yes
  • Feed-forward loop
No No Yes No No No Yes
  • Complete two-layer
No No No No No No Yes
  • Defective clique
No No No No No No Yes
Multiple network operations Yes No No No Yes Yes Yes
User network management Session N/A N/A Individual files Database Individual files Database
  • Network classification
By session N/A N/A No No No By tagging attributes

Note: We have included only some network analysis and visualization systems in this comparison. This list is obviously not exhaustive. Furthermore, since each system has its unique goals, it is not completely fair to compare them in this way. This table simply serves as a quick reference for readers who are interested in knowing some of the differences of the systems.

 
Table S2: Definitions for edge prediction functions.
Function Definition
Couple If the first network contains the edges A->C and B->C, predict that A-B is an edge in the second network.
Sibling If the first network contains the edges A->B and A->C, predict that B-C is an edge in the second network.
Identity If the first network contains the edges A-B, predict that A-B is an edge in the second network.