conserved domain c ombination in protein interaction
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Conserved Domain C ombination In Protein Interaction. Jung, Suk Hoon. October 16, 2009. Contents. Background Conserved Domain Combination GO term evaluation Evaluation on Primary DC for Protein Interaction Discussion. Conserved domain Combination.

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Presentation Transcript
contents
Contents
  • Background
    • Conserved Domain Combination
    • GO term evaluation
  • Evaluation on Primary DC for Protein Interaction
  • Discussion
conserved domain combination
Conserved domain Combination
  • A set of protein domains that has been conserved through evolution
  • A cooperative team in order to realize the function
  • We proposed all-confidence as an index measuring the degree of conservation
  • We found that there are higher correlations between all-confidence and the functional similarity of domains than conventional support or confidence based approach
go term evaluation
GO term Evaluation
  • Gene Ontology term (GO term) describes the function of domains in three categories, molecular function, biological process, cellular component
  • GO term evaluation manifested that function of DC is more correlative with..
    • all-confidence than that with support
    • Molecular function than biological process or cellular component
    • Conserved DC≒ Cooperative DC for molecular function

Pearson’s correlation

r= 0.464

Inner Functional Similarity

Pearson’s correlation

r= 0.205

All-confidence

support

All-confidence

evaluation on primary i nteracting dc pidc
Evaluation on Primary Interacting DC (PIDC)
  • Protein-Protein Interaction (protein binding) is a type of molecular function.
    • PIDC ⊂ Cooperative DC for molecular function(Conserved DC)
  • For the actual example using 3D structures (337 cases)
  • All-confidence Significancy (AS) measures the relative significance (rank) of a DC in relation to other DCs in a protein
    • AS = 1, when the DC has highest all-confidence

All-conf Significancy(dci)

evaluation on primary interacting dc
Evaluation on primary interacting DC
  • AS distinguishes PIDCs from others
    • Type 1 : PIDC (269)
    • Type 2 : subset of PIDC (139)
    • Type 3 : superset of PIDC (938)
    • Type 4 : random DC (5252)
    • Type 5 : non-PIDC (803)

AS

evaluation on primary interacting dc1
Evaluation on primary interacting DC
  • Further consideration
    • 2-member DCs tends to have a higher all-conf than that of 3- member DCs
      • PIDCs have two domains in 297 cases among 337
    • In some protein, all domains participate in PIDC
      • so has no compared DCs
    • Some protein has multiple PIDC according to interaction partner
      • 307 proteins have PIDC in 337 cases
  • New type
    • Type 1 : PIDC
    • Type 2 : random DC
    • Type 3 : non-PIDC
evaluation 1
Evaluation 1
  • 2-member PIDC
  • The number of cases: 269 -> 258
    • # of type 1: 258
    • # of type 2: 237
    • # of type 3: 42

AS

evaluation 2
Evaluation 2
  • After removal of proteins in which all domains participate in PIDC
  • The number of cases: 258 -> 83
    • # of type 1: 83
    • # of type 2: 237
    • # of type 3: 42

AS

evaluation 3
Evaluation 3
  • 30 Proteins use different PIDCs to interact with multiple partners.
  • In them, all PIDCs tend to have high AS, leading to confusion
  • The number of cases: 83-> 65
    • # of type 1: 65
    • # of type 2: 170
    • # of type 3: 27

AS

issue
Issue
  • All-confidence + GO term evaluation + evaluation on PIDC can be reported in a paper
  • Further considerations weaken the evaluation on Primary Interacting DC for PPI
    • Decrease the number of cases to be investigated
    • Blur the functional significance of PIDC compared to other DCs
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