Protein Protein Interactions String Cytoscape

[@Biomeducated]

0:00 Input of 90 genes into STRING database website 1:18 Network stats and expansion of the nodes on the STRING website 5:25 Transfer of the network to CytoScape 8:15 Network analyzer plugin and analysis 15:52 Network style editing Great tutorial! Thank you BB!

[@Bioinformaticswithbb]

Thanks for sharing!

[@Biomeducated]

@@Bioinformaticswithbb No, thank YOU for sharing! ;)

[@yusufceylan104]

Hi! Thank you for this valuable video. I did not understand something, you uploaded 90 sequences and you got 74 nodes, why did you try to increase the number of nodes above 180?

[@masroorahassan5585]

is it okay to extend PPI network and use those results for further research?

[@jamalkhan5752]

hi, how to identify upregulated and downregulated genes in the network?

[@johirislam8174]

Hi,I want to visualize my PPI network into cytoscape.But my ppI node are 661 and edges are 680 and seeds are 15.So i feel problem of visualizing it into cytoscape.Because of huge number of nodes and edges. So how can i visualize this .I mean to say I want to know the way that can visualize all the interacted nodes clearly. Clearly means all the lebels are being clearly watched in manuscript.

[@painpp]

hello nice video, may i ask a question. I have some proteins that interact with each other, i just want to show the interaction between these proteins, please let me know how i can represent the same.

[@shtaahshtaah8262]

I have dataset how can find correlation with gene expression for detecting Alzheimer's disease.plz answer

[@avanimahadik8551]

in the string database why do we need to expand the network? Is it we always expand the network or there is some criteria used? If any such criteria is used can u please tell about that?

[@fengtang6433]

That's what I also want to ask. So many unmeaningful operations. I wasted 20 mins here.

[@caitlingibbons2246]

Hi. Thank you for uploading these videos. I was hoping you could tell me how you obtained the list of up and down regulated genes. Did you use R with Bioconductor along with one, or more, GSE files from the Gene Expression Omnibus? I m working on a class project and I was hoping you could help me. Thank you.

[@jyotibala102]

Great video...Thankyou for sharing

[@Bioinformaticswithbb]

Thanks for watching!

[@manendra3650]

You are concentrating on how to plot graphs but please update us how to understand the data....

[@mominashanwaz]

how to analyze the data in the table?

[@Bioinformaticswithbb]

Hi... this video is just demo of how to use Cytoscape... and it covered briefly on the degree of interactions in between the protein-protein. If u want to analyze whole statistics of the table u have to go through the following link manual.cytoscape.org/en/stable/Network_Analyzer.html

[@aditikonar2411]

I have a set of structurally similar proteins ( that i got in DALI search) so can I study their degree of relatedness this way? Or i also need the substrate with which those proteins interact?

[@Bioinformaticswithbb]

I think Dali will give you known protein structure (Protein Data Bank) results by comparing your protein Query sequence. If you have a group of proteins, yes you can check Protein-protein interactions. The results will elucidate you how protein are interacted together based on proteins Co-occurrence, Co-Expression, Experiments, Databases, Text mining, physical interactions, gene fusion, neighbour genes

[@aditikonar2411]

@@Bioinformaticswithbb thank you so much

[@jyotibala102]

Can you plz upload some online structure prediction tools for DNA 3D structure prediction.

[@Bioinformaticswithbb]

Yes.. Soon

[@jyotibala102]

@@Bioinformaticswithbb Thankyou, we find multiple option for protein through limited tools for 3D nucleic acid....

[@adrianalopez6035]

Thank you so much :')

[@takimsarker929]

nice video. I think the sound quality should be more clear.

[@Bioinformaticswithbb]

its an old video .. now u can see more quality in my videos...

[@kingrock04]

Thanks for the video it's great. But How do you analyze the data in the table? and how is the interpretation and application?

[@Bioinformaticswithbb]

If u want to analyze whole statistics of the table u have to go through the following link manual.cytoscape.org/en/stable/Network_Analyzer.html

[@VibewithSharonAlexander]

Well explained