1. SynechoNET: integrated protein interaction database of Synechocystis
6th InCoB HKUST, Hong Kong
SynechoNET: integrated protein interaction database of Synechocystis
Sungsoo Kang & Jongsoon Choi
Korean BioInformation Center, KRIBB
Korea Basic Science Institute

2. Korean BioInformation Center (KOBIC)
The national bioinformatics center of Korea
Integration of diverse biological information
Genome information
Biodiversity information
Bioresource information
International training programs on bioinformatics
Collaborative development of bioinformatics tools and resources
BioWiki (online knowledge base of biology)
BioPipe (BioWorkflow engine)

3. BioWiki
Wiki
a web technology that enables anyone to create and update website contents.
suited for developing online knowledge bases (e.g., Wikipedia ).
BioWiki
To adopt the wiki paradigm in biology
Collaborative development of biological knowledge bases.
BioWiki Contest ( )

4. BioPipe BioWorkflow Engine BioPipe Contest
No installation required
‘Drag and drop’ supported
BioPipe Contest
Open free Web 2.0
Period: Aug 15th ~ Sep 20th
Website:
Easy way to do bioinformatics 4

5. SynechoNET: integrated protein interaction database of Synechocystis
6th InCoB HKUST, Hong Kong
SynechoNET: integrated protein interaction database of Synechocystis
Sungsoo Kang & Jongsoon Choi
Korean BioInformation Center, KRIBB
Korea Basic Science Institute

6. Cyanobacteria (Synechocystis)
Photosynthetic bacteria with multi-layered membranes
Photo-autotrophic or photo-heterotrophic growth
Ancestor of plant chloroplast

7. Photosynthesis of Synechocystis
Thylakoid membrane contains many phycobilisomes on its surface
Phycobilisomes contain accessory pigments absorbing light for photosynthesis

8. Synechocystis sp. PCC 6803 Model organism of higher plants
Plant-like oxygenic photosynthesis
High transformation efficiency
Light signal transduction mutants
Undergoing systems biology pilot study
‘Genome-to-Life’ project of DOE, USA
The first complete genome sequence among photosynthetic bacteria (DNA Research 1996)
Genome size: 3,573,470 bp, GC content : 47.7%
3167 proteins (92 two-component regulatory proteins)

9. SynechoNET
Provides predicted protein interaction network of Synechocystis sp. PCC 6803
Integrates four complementary and redundant public protein-protein interaction (PPI) databases
Generates prediction reliability based on redundancy
Provides predicted membrane protein information
trans-membrane topology and domain information

10. Overview of SynechoNET System1 2 3 4

11. Web Pages of SynechoNET

12. 1. Integration of Protein Protein Interaction Data
structural interaction
1. Integration of Protein Protein Interaction Data
interaction from multi-contexts

13. Display of predicted protein interactions and their evidences

14. 2. Prediction of Membrane Proteins
Amino acid sequence
Phobius
(HMM model)
Signal peptide
Profile of predicted TM topology and signal peptide
PFAM
(protein domain DB)
Predicted TM topology
Transmembrane (TM) topology
Localizome
(graphic module)
Domain structure

15. Display of predicted transmembrane topology and its evidence

16. 3. External Links from SynechoNET

17. 4-1. Interactive Network Analysis in SynechoNET

18. 4-2. Keyword Search in SynechoNET

19. 4-3. Functional Category Search in SynechoNET

20. Application of SynechoNET
Analysis on highly interacting hub proteins in a specific functional category
Finding upstream or downstream interacting proteins in a cellular pathway
Functional prediction of unknown genes
Analysis on regulatory membrane proteins

21. Interaction Network of Regulatory Proteins (further analysis in Cytoscape program)
No. of found genes: 279
No. of interactions: 2754

22. Highly-Interacting Regulatory Proteins with a Transmembrane Domain

23. Experimental Verification of Predicted Interactions for Further Study
Real interaction verified by yeast two-hybrid analysis
-His
P53 T
Lam
Sll0043
Sll0038
Sll0039

24. Conclusion
SynechoNET: Synechocystis-specific integrated protein-protein interaction (PPI) database with trans-membrane topology and domain information
Integrates PPI information from PSIMAP, iPFAM, InterDom, and STRING
Transmembrane topology and domain information from Phobius and Localizome
Available at or directly at