Overview
description
Transcript of 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.