Biological networks - building and visualizing
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Building, retrieving, visualizing and analyzing biological networks
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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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