Systems Biology Overview

Systems Biology Overview

• Systems biology combines multiple approaches to study complex biological systems
• It focuses on interactions within an organism, not just individual components
• Key components include new software, computation, new data, biology, new biological questions, technology, and new technologies
• The approach relies heavily on network science using mathematical models, physics, and computational power
• Advances in technology improve the quality and quantity of systems biology experiments

Learning Objectives

• Describe systems biology
• State the components of a systems biology analysis
• Identify the parts of a protein-protein network map
• Discuss available protein-protein interaction databases
• Discuss the usefulness of protein-protein networks to research and medicine

Components of a Network

• Networks consist of nodes (individual points) and edges (links between nodes)
• Protein-protein interaction networks contain hubs of interaction
• Similar proteins are likely to act together in complexes due to shared evolutionary functions

Protein-Protein Interactions (PPIs)

• Interaction maps (interactomes) show important proteins
• "Essentialome" proteins are crucial for survival
• These essential proteins frequently cluster
• Understanding how essential proteins interact and contribute to different disease states, and their interactions with non-essential proteins is crucial

Protein Interaction Databases

• Several databases contain protein interaction information. 
• Major databases include STRING, IntAct, and BioGRID
• These databases integrate physical and genetic interaction data, predictions, and information across organisms

IntAct

• IntAct database composition includes physical and other interaction types across multiple species, including humans, yeast, and Arabidopsis.
• The number of interactions in IntAct has increased significantly over time.
• Advantages of IntAct include a significant portion of physical interactions and comprehensive data from multiple mammalian species.
• IntAct includes data from various methods, such as phosphorylation and ubiquitination.

BioGRID

• BioGRID focuses on curated data and detailed yeast interactions.
• Advantages of BioGRID include curated yeast interactions and a combination of high-throughput methods.
• However, it may not have the comprehensive visual outputs of other databases.

STRING

• STRING is a comprehensive database of known and predicted protein-protein interactions, integrating computational predictions and knowledge transfer
• It currently contains interactions involving over 9.6 million proteins from 2,031 organisms
• STRING's advantages are its ease of use, graphical output flexibility, support with references, and combination of experimental data (physical and genetic interactions) and predicted/inferred results

This quiz provides an overview of systems biology, exploring its focus on the interactions among biological components rather than individual parts. You will learn about the key components of systems biology analysis, including network science and protein-protein interaction networks. Understand how advances in technology enhance the quality of experiments in this field.