biological networks - building and visualizing

August 22nd, 2013

Vijayaraj Nagarajan PhD Computational Biologist BCBB/OCICIB/NIAID, National Institutes of Health

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)

Outline

§  Introduc)on to Biological Networks –  Basic components of a network –  Types of Biological networks



§  Available network data –  Integrated interac)on databases –  Searching for interac)on data


§  Demonstra)on –  Building, visualiza)on and analysis of the predicted network (Cytoscape)

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

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

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

Searching for Interac0on Data

STRING IPA

Outline







– Cytoscape – VisANT (Integra)ve Visual Analysis Tool) – Osprey – BioLayout

Popular Visualiza0on Tools

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)

Outline







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

PPI Predic0on Using Microarray Data

§ Melanoma metastasis –  83 samples –  Affymetrix –  GEO –  ARACNE –  geWorkbench –  IP3R1, IP3R2, IP3R3, STIM1, ORAI1

GML File

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

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

Literature Based PPI Predic0on Using Cytoscape

Retrieving PPI Using Cytoscape

Data Visualiza0on, Integra0on, Analysis –  Import ARACNE predicted network –  Import VisANT retrieved network –  Merge all networks –  Mo)f finding

[email protected]

Thank You

biological networks - building and visualizing

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