PROTEIN INTERACTION NETWORK – INFERENCE TOOL

DIVYA RAOCANDIDATE FOR MASTER OF SCIENCE IN

BIOINFORMATICSADVISOR: Dr. FILIPPO MENCZER

CAPSTONE PROJECT PRESENTATIONSCHOOL OF INFORMATICS - INDIANA

UNIVERSITY April 20, 2006

Outline Outline Background PIN-IT Sample Results Future Work References Acknowledgements

• Background• PIN-IT• Sample Results• Future Work• References• Acknowledgements

April 20, 2006

Slide 2 of 19

Definitions

• Proteins are complex, high-molecular weight organic compounds

• Protein interactions are associations between protein molecules

• Examples: enzymes, hormones, transcription factors, antibodies, structural proteins

Outline Background

Definitions PIN-IT Results Future Work References Acknowledgements

April 20, 2006

Slide 3 of 19

Experimental Approaches

• Immunoprecipitation

Outline Background

Experiments

PIN-IT Results Future Work References Acknowledgements

http://www.molecularstation.com/protein/immunoprecipitation/

April 20, 2006

Slide 4 of 19

High Throughput Experiments

• DNA sequence analysis– Homology & Orthology– Limited to proteins encoded by a

single gene in one species or two or more genes in another

Outline Background

Experiments

PIN-IT Results Future Work References Acknowledgements

A a

Species 1

Species 2

April 20, 2006

Slide 5 of 19

a

b

B

bSpecies 3

Yeast Two Hybrid

• Bait & prey • Transcription:

DNA -> RNA• Two haploid

yeasts• Benefit:

– yeast can express genes from almost any species

• Limitation: – Mutations –

false positives– May not

detect weak or rapid interactions

Outline Background

Experiments PIN-IT Results Future Work References Acknowledgements

http://www.biochem.arizona.edu/classes/bioc568/bioc568.htm April 20, 2006

Slide 6 of 19

PRISM Outline Background

Other Tools PIN-IT Results Future Work References Acknowledgements

http

://go

rdio

n.hp

c.en

g.ku

.edu

.tr/p

rism

/tuto

rial.p

hp#p

redi

ctio

ns.p

hp

April 20, 2006

Slide 7 of 19

ADVICE BackgroundOther Tools

http://advice.i2r.a-star.edu.sg/doc/flowchart.gif April 20, 2006

Slide 8 of 19

Motivation

• Interaction maps can be used to reveal drug targets– BCL6 in humans causes B-cell

non-Hodgkin lymphoma. In the fruitfly the BCL6 ortholog binds calcineurin phosphatases

– Hubs vs. peripheral proteins

Outline Background

Motivation PIN-IT Results Future Work References Acknowledgements

April 20, 2006

Slide 9 of 19

Protein Interaction Network Inference Tool

• Infer protein-protein interactions– Known protein interactions– Protein similarity

Outline Background PIN-IT Results Future Work References Acknowledgements

April 20, 2006

Slide 10 of 19

PIN-IT Data sources• Database of Interacting Proteins (DIP)• Biomolecular Interaction Network

Database (BIND) • Proteins with GI numbers, Taxon ID &

experimental source• False positive rate

– Immunoprecipitation, r = 0.1– Yeast Two Hybrid, r = 0.6

Outline Background PIN-IT

Data Sources

Results Future Work References Acknowledgements

April 20, 2006

Slide 11 of 19

Outline Background PIN-IT

Data

DIP BIND PIN-IT

Number of proteins 18826 27809 43573

Number of Interactions 54172 44354 94659

Number of Organisms 109 1020 1033

PIN-IT Data

April 20, 2006

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BLAST• Basic Local Alignment Search Tool

..AGTTAC.. I I I I

..ACTTAG.. • Smith-Waterman algorithm• E-value

– # of different alignments with scores equivalent to or better than S that are expected to occur in a database by chance

• Orthologus proteins• BLASTP

Outline Background PIN-IT

BLAST Results Future Work References Acknowledgements

April 20, 2006

Slide 13 of 19

Calculating Inference

AIB

xy

S

D

),(),(

),(),(),(),(

),(),(

),exp(),(

maxarg),(

1

baba

yBBAxAyx

xAxA

BABA

Dbasuggest

SISD

nES

rI

Where:

r is the false positive rate

E is the e-value from BLAST

n is the size of the dataset

April 20, 2006

Slide 14 of 19

Demo

• PIN-IT

Outline Background PIN-IT

Demo Results Future Work References Acknowledgments

April 20, 2006

Slide 15 of 19

Outline Background PIN-IT Results Future Work References Acknowledgements

April 20, 2006

Slide 16 of 19

Results

63225506324320

63237666321260

Interacts with mRNAs encoding membrane-associated proteins

Putative integral membrane E3 ubiquitin ligase

Putative integral membrane, negative

regulation of amino acid uptake

Has roles in maintenance of cell wall integrity

Future Work

• Allow for the user to upload their protein sequences and interactions

• Better estimation of experimental false positive rates

• Work with biologists to validate the tool and fine-tune the parameters

Outline Background PIN-IT Results Future Work References Acknowledgements

April 20, 2006

Slide 17 of 19

References• Campbell, M. A., Heyer, L.A. Discovering Genomics, Proteomics

& Bioinformatics. India: Pearson Education, 2004, pp176-183.• Ito T, et al.: "A comprehensive two-hybrid analysis to explore

the yeast protein interactome,". Proc Natl Acad Sci 2001, 98:4569-74.

• Titz B, et al.: "What do we learn from high-throughput protein interaction data?". Expert Rev Proteomics 2004, 1:111-21.

• Giot L, et al.: "A protein interaction map of Drosophila melanogaster,". Science 2003 302: 1727-1736

• Aytuna,A.S, Gursoy,A. Keskin,O., (2005). Prediction of protein-protein interactions by combining structure and sequence conservation in protein interfaces. Bioinformatics 21(12):2850-2855

• Tan, Soon-Heng, Zhang, Zhuo, Ng, See-KiongADVICE: Automated Detection and Validation of Interaction by Co-EvolutionNucl. Acids Res. 2004 32: W69-72

• Protein Interactions by Structural Matching (PRISM): http://gordion.hpc.eng.ku.edu.tr/prism/index.php

• Automated Detection and Validation of Interaction by Co-Evolution (ADVICE): http://advice.i2r.a-star.edu.sg/

• DIP: http://dip.doe-mbi.ucla.edu/• BIND: http://www.bind.ca/Action• Immunoprecipitation Image:

http://www.molecularstation.com/protein/immunoprecipitation/• Yeast Two Hybrid system image:

http://www.biochem.arizona.edu/classes/bioc568/bioc568.htm

Outline Background PIN-IT Results Future Work References Acknowledgements

April 20, 2006

Slide 18 of 19

Acknowledgements

• Dr. Filippo Menczer• Dr. Haixu Tang• Dr. Alessandro Flammini• Dr. Sun Kim• Dr. Mehmet Dalkilic• Dr. Gary Wiggins• Linda Hostetter

Outline Background PIN-IT Results Future Work References Acknowledgements

April 20, 2006

Slide 19 of 19

Query

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Query Results

Node Information

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Query Results

Interaction Edge Information

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Query Results

Similarity Edge Information

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Query Results

Inference Edge Information

April 20, 2006