Visualization of Biological Network using Cytoscape

This video tutorial demonstrates integrating biological networks and microarray expression data from STRING and KEGG database using Cytoscape. The Cytoscape software can be freely downloaded from https://cytoscape.org/download.html

Interactomics

Interactomics is the study of interactions and relationship between and within different molecules (DNA, RNA, proteins, ligands, lipids, carbohydrates, etc.). It aims to compare the networks of interactions (interactomes) between and within the species to find the traits of preserved or varied networks.

Types of Biological Networks

List of common biological networks are,
Cell-Cell Interaction Network
Protein–Protein Interaction (PPI) Network
DNA–Protein Interaction Network / Gene Regulatory Network (GRN)
Gene Co-expression Network (GCN) / Transcript–Transcript Association Network
Metabolic Network
Protein–Ligand Interaction Network
Drug-Drug Interaction Network
Disease-Function Association Network
Drug-Side Effect Association Network

Resources for Biological Networks

List of some popular database for biological networks are,
IntAct - https://www.ebi.ac.uk/intact/
STRING - https://string-db.org/
KEGG - https://www.genome.jp/kegg/
BioModels - https://www.ebi.ac.uk/biomodels/
InnateDB - https://www.innatedb.com/
TRRUST - https://www.grnpedia.org/trrust/
BioSNAP - http://snap.stanford.edu/biodata/
ReactomeFI - https://reactome.org/
Gene Ontology - http://geneontology.org/
GEO - https://www.ncbi.nlm.nih.gov/geo/
ArrayExpress - https://www.ebi.ac.uk/arrayexpress/
miRNet - https://www.mirnet.ca/
JASPAR - http://jaspar.genereg.net/
ENCODE - https://www.encodeproject.org/
BioCyc - https://biocyc.org/
SMPDB - https://smpdb.ca/
MatrixDB - http://matrixdb.univ-lyon1.fr/
SPIKE - https://www.cs.tau.ac.il/~spike/
NetPath - http://www.netpath.org/

Cytoscape Supported Network File Formats

Cytoscape can read network/pathway files written in the following formats:
Simple interaction file (SIF or .sif format)
Nested network format (NNF or .nnf format)
Graph Markup Language (GML or .gml format)
XGMML (extensible graph markup and modelling language).
SBML (Systems Biology Markup Language)
BioPAX (Biological Pathway Exchange)
GraphML (Graph XML)
Delimited text (space, tab, CSV, etc.)
Excel Workbook (.xls, .xlsx)
Cytoscape.js JSON
Cytoscape CX

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#Cytoscape #BioGem #biogem.org #BioBIN #biob.in #Bioinformatics #AKBIT #IntAct #STRING #KEGG #BioModels #InnateDB #TRRUST #BioSNAP #ReactomeFI #GeneOntology #GEO #GO #ArrayExpress #miRNet #JASPAR #ENCODE #BioCyc #SMPDB #MatrixDB #SPIKE #NetPath #SBGN