Title: PutidaNET : Interactome database service and network analysis of Pseudomonas putida KT2440
1 PutidaNET Interactome database
service and network analysis of
Pseudomonas putida KT2440 (P. putida KT2440)
Korean BioInformation Center
(KOBIC)
Seong-Jin, Park
2Pseudomonas 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.
3Why 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.
4What 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.
5Overview of PutidaNET system
NCBI
PEIMAP
Protein interaction analysis
PSIMAP
iPfam
PutidaNET
P. Putida KT2440
GO
Functional annotation
KEGG
6Protein-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
7Functional 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
8PutidaNET 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- p(1-Ri)3 1-
(1-RPEIMAP)(1-RPSIMAP)(1-RiPfam) I
Interaction method used R Reliability of each
method
9PutidaNET 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
S
B-S
S-B
BnS
66
806
514
-gt Benzoate -gt Succinate
-gt Intersection set of succinate and benzoate
-gt No information
10PutidaNET 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.
11Web interface
NP_742815.1
12Web interface
Interaction partners
13Web interface
14Web interface
15PutidaNET
- 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