Question: Filter out the information from other organisms in STRING
0
gravatar for Xiaokang ZH
2.6 years ago by
Xiaokang ZH50
Xiaokang ZH50 wrote:

I'm using STRING to get the interaction between some interesting genes in cod (Gadus morhua). On the page of "search", you can choose the organism you're interested in, and STRING will only give you the genes that they have a record in their database for cod, which is what I want. And then you'll get a network including the genes in your list. When you look into the links, and here's an example, you'll get "Relevant publications mentioning your query species (Gadus morhua)", and instead, they provide "Relevant publications mentioning other organisms"; and here's another example, it's a similar case. I guess that there's very limited information about cod, so STRING will borrow the information from other organisms that have the homologous genes. But is there a way to filter out the "borrowed" information? Or to say, I only want to have the interactions in "Relevant publications mentioning your query species (Gadus morhua)" in the first example or "Relevant datasets in Gadus morhua" in the second example.

string ppi • 643 views
ADD COMMENTlink written 2.6 years ago by Xiaokang ZH50
1

how about downloading the data and filtering the text files ? https://string-db.org/cgi/download.pl

ADD REPLYlink written 2.6 years ago by Pierre Lindenbaum131k

Thank you! From the webpage you provide, there's a file "protein.links.full", where it provides scores from different channels, and there will be two columns for each channel. For an example, "database" and "database_transferred" for the specific species itself and information from other species (putative homologs are reported to interact in other species) respectively. So if I want to avoid information from other species, I guess that I can simply remove the "*_transferred" columns.

ADD REPLYlink modified 2.6 years ago • written 2.6 years ago by Xiaokang ZH50

Hello Xiaokang ZH!

It appears that your post has been cross-posted to another site: https://stackoverflow.com/questions/49514657

This is typically not recommended as it runs the risk of annoying people in both communities.

ADD REPLYlink written 2.6 years ago by Pierre Lindenbaum131k

Hi Pierre, thank you for reminding. The other post is now deleted.

ADD REPLYlink written 2.6 years ago by Xiaokang ZH50
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