Problem with link generated with R using the string_db$get_link
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@ilario-de-toma-5961
Last seen 4.5 years ago
Italy

I have always been using those commands in R for getting my protein network to be visualized in the string-db site.

However now only the first protein of the list get visualized.

> head(list_wttg)
  list_wttg logFC
1    A2A5R2     2
2    A2AJA9     2
3    O88703     2
4    O88737     2
5    P06837     2
6    P0C7M9     2

string_db <- STRINGdb$new(version="10",species=10090,score_threshold=400, input_directory="" )mapped <- string_db$map( list_wttg, "list_wttg", removeUnmappedRows = FALSE )

mapped <- string_db$add_diff_exp_color( mapped, logFcColStr="logFC" )

payload_id <- string_db$post_payload( mapped$STRING_id,
 colors=mapped$color )

string_db$plot_network( mapped$STRING_id, payload_id=payload_id )
string_db$get_link( mapped$STRING_id)

string-db.org/10/p/9425227685

 

By putting this link on the browser "string-db.org/10/p/9425227685" I get redirected to this page:

http://string-db.org/version_10/newstring_cgi/go.pl?id=9425227685

that is telling me that 261 proteins are detected in Mus musculus,  1 in Drosophila melanogaster, 1 in Lawsonia intracellularis, and 1 in Danaus plexippus. When I select "Mus musculus" and click on "continue", the first protein get recognized but all the others not:

 

'10090.ENSMUSP00000096677':

Arfgef2 - ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited); Promotes guanine-nucleotide exchange on ARF1 and ARF3 and to a lower extend on ARF5 and ARF6. Promotes the activation of ARF1/ARF5/ARF6 through replacement of GDP with GTP. Involved in the regulation of Golgi vesicular transport. Required for the integrity of the endosomal compartment. Involved in trafficking from the trans-Golgi network (TGN) to endosomes and is required for membrane association of the AP-1 complex and GGA1. Seems to be involved in recycling of the transferrin receptor from recycling [...]

'0D10090.ENSMUSP00000109855':

- - Sorry, STRING found no proteins by this name in Mus musculus - -

 

I guess it is for this "0D" suffix which is added before the protein identifier. I do not know why this happens because on my R "mapped" object there is not:

 

> head(mapped)
  list_wttg logFC                STRING_id     color
1    A2A5R2     2 10090.ENSMUSP00000096677 #FFBABAFF
2    A2AJA9     2 10090.ENSMUSP00000109855 #FFBABAFF
3    O88703     2 10090.ENSMUSP00000020581 #FFBABAFF
4    O88737     2 10090.ENSMUSP00000035208 #FFBABAFF
5    P06837     2 10090.ENSMUSP00000099881 #FFBABAFF
6    P0C7M9     2 10090.ENSMUSP00000110524 #FFBABAFF
stringdb • 585 views
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