Download PutidaNET : Interactome database service and network analysis of

PutidaNET
:Interactome database service and network analysis of
Pseudomonas putida KT2440 (P. putida KT2440)
Korean BioInformation Center (KOBIC)
Seong-Jin, Park
Pseudomonas putida (P. putida)
• A ubiquitous bacterium which can break down
a variety of organic materials for food.
• Plays vital role in recycling of organic wastes and degradation of
biogenic and xenobiotic pollutants present in the environment.
• A model organism for genetic and physiological studies and for
the development of biotechnological applications.
Why Protein Interactome is important?
• To provide valuable insights into biological functions and
processes in cells.
• To provide important clues about how to interpret metabolic
pathways of enzymes.
What is PutidaNET?
• Comprehensive interaction database which provides predicted
protein-protein interaction information of P. putida
• A web server that provides various kinds of functional information such
as physico-chemical properties, biological pathways, and gene
ontology of protein.
Overview of PutidaNET system
PEIMAP
NCBI
Protein
interaction
analysis
PSIMAP
iPfam
P. Putida
KT2440
PutidaNET
Functional
annotation
GO
KEGG
Protein-protein interaction prediction methods
•
PSIMAP (Protein Structural Interaction)
The interactions among proteins by using BLASTP algorithm with a common expectation
value (0.0001).
•
PEIMAP (Protein Experimental Interaction)
Integrating various experimental protein-protein interaction database such as BIND, DIP,
MINT, HPRD and BioGrid.
•
iPfam
Alignment of Pfam domains of all the P. putida proteins with hmmpfam by the cut-off of
expectation value (0.01).
PSIMAP & PEIMAP
Functional annotation
• The biological function information using KEGG and GO
databases.
• General information about proteins such as hydropathy scores,
subcellular- localization, GRAVY score, and protein instability
index.
 Provides valuable insight into protein functions and help to
understand the PPI networks of P.putida
PutidaNET statistics
• 3,254 proteins for P. putida KT2440, contains 82,019 predicted
PPI partners.
• PPIs are ranked by confidence score base on reliability.
Confidence Score = 1- π(1-Ri)3
= 1- (1-RPEIMAP)(1-RPSIMAP)(1-RiPfam)
I : Interaction method used
R : Reliability of each method
PutidaNET case study (1/2)
• We integrated PPI network with experimental 2 DE/MS-MS data.
• We then acquired the protein lists in culture media including
succinate and benzoate.
B
B-S
66
-> Benzoate
-> Succinate
-> Intersection set of succinate and benzoate
-> No information
S
B∩S
806
S-B
514
PutidaNET case study (2/2)
Y axis : Degree Score
X axis : Cultured media in carbon source
• We calculated the degree score for the network.
• We found that the main protein network of P.putida is regulated by
an intersection set of succinate and benzoate.
Web interface
NP_742815.1
Web interface
Interaction partners
Web interface
Web interface
PutidaNET
• An integration of mutually complementary protein-protein
interactions for the systematic analysis of P. putida.
• Provide the highly predicted PPIs by ranking using
confidence score
• Researchers to access and obtain information through an
automatic annotation for queried protein.
• PutidaNET: http://sequenceome.kobic.kr/PutidaNET