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Korean BioInformation Center (KOBIC)

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 ).

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Korean BioInformation Center (KOBIC)

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  1. PutidaNET :Interactome database service and network analysis ofPseudomonas 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- π(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 B∩S 806 66 514 • -> Benzoate • -> Succinate • -> Intersection set of succinate and benzoate • -> 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 ofP. 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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