Visualization of Biological Network using Cytoscape
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- Опубликовано: 15 янв 2025
- 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 cytoscape.org/...
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 - www.ebi.ac.uk/...
STRING - string-db.org/
KEGG - www.genome.jp/...
BioModels - www.ebi.ac.uk/...
InnateDB - www.innatedb.com/
TRRUST - www.grnpedia.o...
BioSNAP - snap.stanford.e...
ReactomeFI - reactome.org/
Gene Ontology - geneontology.org/
GEO - www.ncbi.nlm.n...
ArrayExpress - www.ebi.ac.uk/...
miRNet - www.mirnet.ca/
JASPAR - jaspar.genereg....
ENCODE - www.encodeproj...
BioCyc - biocyc.org/
SMPDB - smpdb.ca/
MatrixDB - matrixdb.univ-l...
SPIKE - www.cs.tau.ac....
NetPath - 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
Great sir, Awesome video content and resource links, Best wishes.
Thank you for your wishes.
Thank you Sir for the detailed explanation.
Please in the WGCNA gene-coexpression network construction, which of the attributes (i.e gene name, the module colour, degree, strength, closeness, betweenness) are used in building the Cytoscape data or edge list. I have followed all the referral links you suggested but most seem to use the film -actor data.
Thank you
Try the data available at horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/WGCNA/Tutorials/
Very accurate and complete video, my deepest compliments! Could you please film a video explaining how to obtain dynamic networks, working with Cytoscape? Thank you in advance
Sure thing! I'll try to post soon.
hi can you explain how I can make a gene interaction( to make a net work with some genes )in cytoscape???
Refer the following link miriamposner.com/classes/dh201w19/tutorials-guides/network-analysis/create-a-network-graph-with-cytoscape/
Geat job, Would you please prepare triple network visualization as miR-mRNA-lncRNA?
Sure. I'll post soon. Do you mean lncRNA-miRNA-mRNA network?
@@AKBIT yes I mean the triple targeting network as lncRNA/miRNA/mRNA via using Cytoscape and how to set up and insert the excel file the Cytoscape. it will be helpful to many researchers, appreciation and a lot of thanks
Very well done
Thank you for your feedback 🙂
Nice and informative videos. keggscape is not installing in cytoscape. please help
I have just now tried to install KEGGscape. There are no issues and working fine.
Try after updating Cytoscape or Run as administrator.
Ossam.....sir
Thank you
Hi .iam from iraq can help me in cytoscape
Sure.. How can I help you?
Hello sir can you give more detailed explanation of this?
To study the relationship among various biomolecules through different network models. The relationship may be molecular interactions or sequence similarities.
@@AKBIT sir i want to know how to create Excel files for creating a network
@@saikulkarni7867 Refer the following link miriamposner.com/classes/dh201w19/tutorials-guides/network-analysis/create-a-network-graph-with-cytoscape/
@@AKBIT sir your amazing ♥️♥️♥️ thank you ♥️😌
@@saikulkarni7867 Thank you
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