1 / 11

Conserved Domain C ombination In Protein Interaction

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.

dora-doyle
Download Presentation

Conserved Domain C ombination In Protein Interaction

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript


  1. Conserved Domain CombinationIn Protein Interaction Jung, SukHoon October 16, 2009

  2. Contents • Background • Conserved Domain Combination • GO term evaluation • Evaluation on Primary DC for Protein Interaction • Discussion

  3. 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

  4. 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

  5. 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)

  6. 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

  7. 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

  8. Evaluation 1 • 2-member PIDC • The number of cases: 269 -> 258 • # of type 1: 258 • # of type 2: 237 • # of type 3: 42 AS

  9. 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

  10. 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

  11. 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

More Related