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Overlay genes with shared phenotypes onto StringDB networks

 

This functionality allows the user to extract a list of UniProt IDs for genes that share a given phenotype within a screen, and to send this list directly to StringDB, a database that stores known gene/protein interactions.

In this way, functional interactions suggested by the given RNAi experiment can be overlaid onto other known interactions and further explored. For documentation of the functionalities of the StringDB website, see here.

It is also possible to extract a list of UniProt IDs mapping to genes sharing a given phenotype, for individual further analyses (see below).

 

 

Request to send a list of UniProt IDs to StringDB directly

When displaying a screen with its phenotypes, move your mouse over the phenotype bar to display two links, "UniProtIDs" and "StringDB". Clicking on "StringDB" extracts all the UniProt IDs mapping to the genes that show the given phenotype and sends this list directly to the StringDB website.

NOTE: the number of UniProt IDs can considerably exceed the number of genes indicated in parentheses, due to multiple mappings. If the number of UniProt IDs is too high (about > 400), the automatic transfer to StringDB becomes unreliable or leads to an error. In this case you should use the manual extraction of the UniProt ID list as described below.

 

 

On the StringDB website, the transmitted UniProt IDs are listed, along with the information as to whether the given ID has been found in the String database. This page allows the user to exclude proteins from the list.

Clicking on "Continue" displays all mapped proteins and any known interactions between them. StringDB allows the user to apply filters, run enrichment analyses, etc. For further information consult the StringDB documentation.

 

 

Extract a list of UniProt IDs

Here you can extract a list of all UniProt IDs mapping to the genes sharing the selected phenotype in a screen.

You may choose to use this method when the direct transfer to StringDB isn't an option due to a high number of IDs (see above), or you may want to use this list for other analyses.

If you want to overlay your list of UniProt IDs onto StringDB networks, extract the list of UniProt IDs by clicking on the "UniProtIDs" link (see above). Go to the StringDB website and choose the tab "multiple names". Then copy and paste your IDs into the text field and follow the instructions.

 

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