Overview

Overview

Introduction Biological network data Text mining Gene Ontology Expression data basics Expression, text mining, and GO Modules and complexes

Domains and conclusion

Domain Interaction networks

Protein domain basicsApplications of domain interaction

networksInferring domain interaction

networksDomain interaction networks in

Cytoscape.

Facts about protein structure

1. Protein structures are built from domains.

2. Domain composition implies protein function.

Protein domains come in families

Domains can be recognized through sequence similarity

Source: http://www.sbg.bio.ic.ac.uk/ people/rob/sf/sf.html

Interactions are often domain-specific

Source: http://faculty.umdnj.edu/ cabm/faculty_stock.asp

Why study protein domain interactions?

A putative protein-protein interaction is more reliable if the proteins have domains that might interact.

If something disrupts the protein sequence, it might disrupt the domain, and thus the networkGenetic or somatic mutationsSplice variation

Exon Intron Intron IntronExon Exon Exon

DNA

Pre-mRNA

TranscriptionTranscription

mRNA

SplicingSplicing

Protein

TranslationTranslation

Single Protein-Protein Interaction

Structural Protein Domain Architecture

UBL UBA XPC UBA

Which part of the proteins interact?

1. Protein structure: which domain structures are complementary?

2. Domain co-occurrence: which domains tend to appear in the same proteins?

3. Rosetta stone: are any domains fused in other proteins?

4. Yeast two-hybrid domain interactions: coming soon.

Which part of these proteins interact?

Josephin UIM UIM

!!

UBL UBA XPC UBA

Databases such as InterDom provide putative interactions of Pfam domains

Domain interaction networks

For this hands-on session

Explore usage of the Cytoscape Domain Network builder plugin

Fill out your evaluation sheets.