LinkedPPI: Enabling Intutive, Integrative Protein-Protein Interaction Discovery
Laleh Kazemzadeh, Maulik R.Kamdar, Oya D.Beyan,Stefan Decker, Frank Barry
19-10-2014
Outline
IntroductionMotivation and Challenges
MethodsLinkedPPI architectureDomain-Specific Model
ResultsSearch and VisualizationUse Cases
Summary
Challenges
Human genome contains 20000 protein coding genes
Number of binary interaction 2^20000
Incomplete knowledge of the underlying networks What we don’t know that we don’t know
Massive amount of data with too many “standards”
Method: LinkedPPI Architecture
Data Source Ineraction # Interactions # Triples
BioGRID Protein-Protein 634996 11357231
CORUM Complex 2867 156364
3did Domain-Domain 61582 320690
Use case1: Extraction of Protein-Protein Interaction Based on Domain-Domain Interactions
Let’s Assume a single protein e.g. HES1Q1: What are the potential interacting partners?
What we know: It contains a protein domain called Hairy_orange
We know Hairy_orange’s interacting domains
What we can retrieve: List of proteins that contains the protein domains which are known to be Hairy_orange interacting domains.
Use Case2: Identification of Potential Domain-Domain Interaction
Let’s assume a protein domain e.g. HLH Q2: What are its interacting domains?
What we know:List of validated domain partners for
HLHList of validated protein pairs which
contains HLH What we can retrieve:
One-to-One domain interaction for HLH
One-to-Many domain interactions for
HLH
Use Case3: Identification of Selective Interactions between Segments of Human Genome
Biological Facts: Chromosomes are folded in territory Genes in closer proximity tends to be co-expressed Interacting proteins tend to have common functionality
What we have:List of validated protein interactions
Genomic location of each protein (start and stop position of the coding gene)
What we can infer: The frequency in which each two segments of genome appear to be interacting
Summary
Domain-Specific Model
Search and Visualization
3 Use Cases
Link to the public Endpoints(e.g.EBI)
Statistical Analysis on the Significance of the Results
Classification of Interacting and non-Interacting Pairs
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