Basic stringApp tutorial: Cytoscape app store, STRING protein query, and omics data visualization

[@abeer8733]

Really helpful video and very well explained! Best of luck 💖

[@larsjuhljensen]

Thank you very much, I'm happy you found it helpful!

[@larapanfilov369]

Why can't I see the continuous mapping option for my log2 fold change? It only gives me the discrete or passthrough options

[@larsjuhljensen]

Check the data type of the column in your node table. Chances are that you got the data imported as text strings instead of as numbers (you cannot do a continuous mapping of strings).

[@larapanfilov369]

@@larsjuhljensen Thank you for the help. It works now. Just a quick question, if I input 200 genes in the query search and it only shows searching for 142 identifiers, what is the exact problem?

[@larsjuhljensen]

You either had redundant gene names, i.e. multiple names for the same gene/protein, or you had names that could not be mapped. The latter is more likely to be your problem. If you can, try querying with something like UniProtKB identifiers or accession numbers, which should give you less mapping issues than gene symbols.

[@larapanfilov369]

@@larsjuhljensen What do you exactly mean by that? I am putting in the Gene Symbols. I could use a gene ID as well but I would like to see the gene IDs in the glass balls. Thanks again for all the help!

[@larsjuhljensen]

The names shown is not linked to which terms you use for doing the search. By default, the names that are shown are the "STRING display names" of the proteins found in the query, not the names or identifiers that you used to search with. And if you want the gene symbols from your own table to be shown, the best way is to (after querying) import your table to the node table and set the node labels to be whichever column in the table you want.

[@virgirma1328_PhD_scholar]

Good morning teacher.Thanks for the educative content. Could you please indicate which version of Cytoscape you are using for the above tutorial?

[@larsjuhljensen]

It was probably Cytoscape 3.9.x given when it was recorded, but not much should have changed to the current 3.10.x version.

[@videosdocentesuniovi8503]

Really interesting. Many thanks!

[@larsjuhljensen]

You are very welcome - I'm planning a similar tutorial quite soon on how to visualize more complex data with the Omics Visualizer app.

[@videosdocentesuniovi8503]

@@larsjuhljensen Great! Thanks for guiding us. Its really interesting String app. I was aware by Jonas Grossmann at the FGC of Zurich. I am very happy using it. Regards!

[@shtaahshtaah8262]

Hi sir ,can help me with cytoscsape

[@larsjuhljensen]

If you haven't already, I suggest you first go through jensenlab.org/training/stringapp/ If you have more general questions to how to solve a certain problem in Cytoscape, the Cytoscape help desk would be the best place to ask: groups.google.com/g/cytoscape-helpdesk

[@germanrosano2152]

Hi Lars, great tutorial. What would you say is the main difference between stringApp and Omics Visualizer?

[@larsjuhljensen]

They are entirely different apps. We designed stringApp to allow you to easily retrieve STRING networks and gives you access to other functionality of STRING, such as enrichment analysis. Omics Visualizer extends the data visualization functionality of Cytoscape so that you can visualize multiple values on each node (think phosphorylation sites and/or time courses) regardless of whether the network came from STRING or not. We of course designed the two apps to play nicely together, which means that you can easily retrieve a STRING network from Omics Visualizer, which is does by asking stringApp to do it.

[@germanrosano2152]

@@larsjuhljensen Thanks!

[@JuneRacoon]

Thanks!

[@larsjuhljensen]

You're welcome!