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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Conserved domain c ombination in protein interaction

Conserved Domain CombinationIn Protein Interaction

Jung, SukHoon

October 16, 2009


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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