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
