PutidaNET : Interactome database service and network analysis of Pseudomonas putida KT2440 - PowerPoint PPT Presentation

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PutidaNET : Interactome database service and network analysis of Pseudomonas putida KT2440

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Pseudomonas putida KT2440 (P. putida KT2440) Korean BioInformation Center (KOBIC) ... Pseudomonas putida (P. putida) A ubiquitous bacterium which can break down ... – PowerPoint PPT presentation

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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
2
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.

3
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.

4
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.

5
Overview of PutidaNET system
NCBI
PEIMAP
Protein interaction analysis
PSIMAP
iPfam
PutidaNET
P. Putida KT2440
GO
Functional annotation
KEGG
6
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
7
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

8
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- p(1-Ri)3 1-
(1-RPEIMAP)(1-RPSIMAP)(1-RiPfam) I
Interaction method used R Reliability of each
method
9
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
S
B-S
S-B
BnS
66
806
514
-gt Benzoate -gt Succinate
-gt Intersection set of succinate and benzoate
-gt No information
10
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.

11
Web interface
NP_742815.1
12
Web interface
Interaction partners
13
Web interface
14
Web interface
15
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
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