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Lecture 7 Protein Protein Interaction Database

This document discusses protein-protein interactions and databases that contain information about them. It explains that most proteins interact with other proteins to function properly and that interactions can be stable or transient. It provides examples of several major protein-protein interaction databases like BioGRID and STRING as well as biological pathway databases like Reactome and KEGG that organize interaction data into biological pathways. The document also outlines some of the methods like co-expression analysis that STRING uses to predict protein-protein interactions.

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Bhawna Rathi
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26 views

Lecture 7 Protein Protein Interaction Database

This document discusses protein-protein interactions and databases that contain information about them. It explains that most proteins interact with other proteins to function properly and that interactions can be stable or transient. It provides examples of several major protein-protein interaction databases like BioGRID and STRING as well as biological pathway databases like Reactome and KEGG that organize interaction data into biological pathways. The document also outlines some of the methods like co-expression analysis that STRING uses to predict protein-protein interactions.

Uploaded by

Bhawna Rathi
Copyright
© © All Rights Reserved
Available Formats
Download as PPTX, PDF, TXT or read online on Scribd
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Topic Name – Protein-Protein Interaction

Database
BACKGROUND
• What is Protein-Protein Interaction?
 Proteins are the workhorses that facilitate most biological processes in a
cell, including gene expression, cell growth, proliferation, nutrient uptake,
morphology, motility, intercellular communication and apoptosis.
 Until the late 1990's, protein function analyses mainly focused on single
proteins. But because the majority of proteins interact with other proteins
for proper function, they should be studied in the context of their
interacting partners to fully understand their function.
 Protein interactions are fundamentally characterized as stable or
transient, and both types of interactions can be either strong or weak.
 Stable interactions are those associated with proteins that are purified as
multi-subunit complexes, and the subunits of these complexes can be
identical or different. Hemoglobin and core RNA polymerase are
examples of multi-subunit interactions that form stable complexes.
BACKGROUND
• Transient interactions are expected to control the majority of
cellular processes. As the name implies, transient interactions
are temporary in nature and typically require a set of
conditions that promote the interaction, such as
phosphorylation, conformational changes or localization to
discrete areas of the cell.
• Proteins bind to each other through a combination of
hydrophobic bonding, van der Waals forces, and salt bridges
at specific binding domains on each protein.
PROTEIN-PROTEIN INTERACTION (PPI) AND
BIOLOGICAL PATHWAYS (BP) DATABASES
• There are two kinds of databases, each concentrate on one of
the two aspects of the biochemical/biological data:
• (i) Protein-protein interaction (PPI) databases gather data on
the physical interactions between proteins.
• (ii) Biological pathways (BP), databases including metabolic
and transport pathways , signaling cascades, and regulation
networks, gather data on the biological meaning of PPIs and
other possible interaction between gene products.
• Most of these two kinds of databases enable visualization and
producing of maps showing a selected group of interactions.
EXAMPLES FOR PPI AND
BIOLOGICAL PATHWAYS DATABASES
• PPI databases
 BIOGRID (http://thebiogrid.org)
 STRING (http://stringdb.org)
 APID
 Dip (http://dip.doe-mbi.ucla.edu/)
 MINT (http://mint.bio.uniroma2.it/mint/Welcome.do)
 INTERACTOME (http://www.ebi.ac.uk/intact/main.xhtml)
 HPRD (http://hprd.org/)
 BIND (http://bind.ca/)
• Biological Pathways Databases
 REACTOME (http://www.reactome.org/)
 KEGG (http://www.genome.jp/kegg/)
STRING

Genomic Neighborhood

Genes/Species Co-occurence

Gene Fusions

Database Imports

Exp. Interaction Data

Co-expression

Literature co-occurence
OTHER RESOURCES
Interaction Databases Pathway Databases
Reactome

Automated Textmining Interolog Transfer

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