Download - Korean BioInformation Center (KOBIC)
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PutidaNET :Interactome database service and network analysis of
Pseudomonas putida KT2440 (P. putida KT2440)
Korean BioInformation Center (KOBIC) Seong-Jin, Park
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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.
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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.
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• 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.
What is PutidaNET?
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Overview of PutidaNET system
Functional annotation
Protein interaction
analysis
PutidaNET
PEIMAP
PSIMAP
iPfam
KEGG
GO
NCBI
P. Putida KT2440
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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
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• 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
Functional annotation
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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
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• We integrated PPI network with experimental 2 DE/MS-MS data.
• We then acquired the protein lists in culture media including succinate and benzoate.
PutidaNET case study (1/2)
-> Benzoate
-> Succinate
-> Intersection set of succinate and benzoate
-> No information
B S
B-S S-BB∩S
66 806 514
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PutidaNET case study (2/2)
• 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.
Y axis : Degree ScoreX axis : Cultured media in carbon source
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Web interface
NP_742815.1
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Web interface
Interaction partners
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Web interface
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Web interface
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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