Biological networks - building and visualizing
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The document outlines Vijayaraj Nagarajan's presentation on biological networks. It will cover an introduction to biological networks, predicting and building networks, available interaction data sources, network visualization and analysis tools, and a demonstration of building, visualizing and analyzing a predicted biological network using Cytoscape. Prediction methods that will be discussed include using microarray data with algorithms like ARACNE. Popular visualization tools mentioned are Cytoscape and VisANT.
Biological networks - building and visualizing
- 1. August 22nd, 2013 Vijayaraj Nagarajan PhD Computational Biologist BCBB/OCICIB/NIAID, National Institutes of Health
- 2. Outline § Introduc)on to Biological Networks – Basic components of a network – Types of biological networks § Predic)ng/Building Biological Networks – Methods • Logic and concept § Available Interac)on data – Integrated protein-‐protein interac)on databases – Searching for interac)on data § Network Visualiza)on and Analysis tools – Popular visualiza)on tools – Network analysis § Demonstra)on – Building, visualiza)on and analysis of the biological networks (Cytoscape)
- 3. Outline § Introduc)on to Biological Networks – Basic components of a network – Types of Biological networks § Predic)ng/Building Biological Networks – Methods • Logic and concept § Available network data – Integrated interac)on databases – Searching for interac)on data § Network Visualiza)on and Analysis tools – Popular visualiza)on tools – Network analysis § Demonstra)on – Building, visualiza)on and analysis of the predicted network (Cytoscape)
- 4. Available Interac0on Network Data § MINT – Molecular Interac)on Database § BIND * – Biomolecular Interac)on Network Database § DIP – Database of Interac)ng Proteins § IntAct – InterAc)on Database at EBI
- 5. Integrated Data Sources § Pathway Commons § BioGRID § MiMI (Michigan Molecular Interac)ons) § STRING (Search Tool for Retrieval of Interac)ng Genes/Proteins) § Genes2Network § VisANT (Integra)ve Visual Analysis Tool) § GeneMANIA § BIOBASE § IPA (Ingenuity Pathway Analysis) § MetaCore Open Source Proprietary
- 6. IP3Rs § Inositol triphosphate receptor – ip3r1 – ip3r2 – ip3r3 • Calcium ion channels • ER – s)m1 (stromal interac)on molecule 1) • PM • Calcium sensor protein – orai1 (calcium release ac)vated calcium modulator) • PM • Accessory protein downstream of s)m1
- 7. Searching for Interac0on Data STRING IPA
- 16. IPA
- 23. Outline § Introduc)on to Biological Networks – Basic components of a network – Types of Biological networks § Predic)ng/Building Biological Networks – Methods • Logic and concept § Available network data – Integrated interac)on databases – Searching for interac)on data § Network Visualiza)on and Analysis tools – Popular visualiza)on tools – Network analysis § Demonstra)on – Building, visualiza)on and analysis of the predicted network (Cytoscape)
- 24. – Cytoscape – VisANT (Integra)ve Visual Analysis Tool) – Osprey – BioLayout Popular Visualiza0on Tools
- 25. Analysis Tools § Phunkee (Pairing subgraphs Using Network Environment Equivalence – finds similar subnets) § mfinder (mo)f detec)on) § MAVisto (Mo)f Analysis and Visualiza)on tool – explora)on of mo)fs) § GraphMatch (Search for similar sub-‐nets) § NeAT (Network Analysis Tools – mo)f finding, node sta)s)cs) § Cfinder (Finds clusters – dense group of nodes) § NetworkBLAST (Compares mul)ple networks to infer complexes & paths)
- 26. Outline § Introduc)on to Biological Networks – Basic components of a network – Types of Biological networks § Predic)ng/Building Biological Networks – Methods • Logic and concept § Available network data – Integrated interac)on databases – Searching for interac)on data § Network Visualiza)on and Analysis tools – Popular visualiza)on tools – Network analysis § Demonstra)on – Building, visualiza)on and analysis of the predicted network (Cytoscape)
- 27. PPI Predic0on Using Microarray Data § Co-‐expression concept – Correla)on Coefficient • SIMoNE (Sta)s)cal Inference for Modular Networks) -‐ R – Mutual Informa)on • Reference Networks • ARACNE (Algorithm for Reconstruc)on of Accurate Cellular Networks) – R, geWorkbench • CLR (Context Likelihood of Relatedness) – R • MRNET (Maximum Relevance/Minimum Redundancy) – R • MONET (Modularized NETwork Learning) -‐ Cytoscape – Bayesian Network
- 28. PPI Predic0on Using Microarray Data § Melanoma metastasis – 83 samples – Affymetrix – GEO – ARACNE – geWorkbench – IP3R1, IP3R2, IP3R3, STIM1, ORAI1
- 40. GML File
- 41. Predicted PPI Network § Could form a complex § Could be func)onally associated § Could be involved in a same metabolic pathway § Could be involved in a specific signal transduc)on path § False posi)ve
- 42. Visualiza0on and Analysis Using Cytoscape § Cytoscape – Opensource – Works in Windows, Linux, Mac – One of the first developed tools – Great number of PLUGINS – Excellent help from community
- 43. Literature Based PPI Predic0on Using Cytoscape
- 47. Retrieving PPI Using Cytoscape
- 51. Data Visualiza0on, Integra0on, Analysis – Import ARACNE predicted network – Import VisANT retrieved network – Merge all networks – Mo)f finding
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