Question: what information can I obtain from a bunch of proteins IDs?
0
gravatar for Mo
5.0 years ago by
Mo920
/
Mo920 wrote:

hello,

 

Lets say I have a large of Proteins IDs as follows:

sp|A3KN83|SBNO1_HUMAN
sp|A6NHQ2|FBLL1_HUMAN
sp|E9PRG8|CK098_HUMAN
sp|O00115|DNS2A_HUMAN
sp|O00151|PDLI1_HUMAN
sp|O00170|AIP_HUMAN
sp|O00178|GTPB1_HUMAN
sp|O00267|SPT5H_HUMAN
sp|O00303|EIF3F_HUMAN
sp|O00418|EF2K_HUMAN
sp|O00571|DDX3X_HUMAN;sp|O15523|DDX3Y_HUMAN;sp|Q9NQI0|DDX4_HUMAN
sp|O00629|IMA3_HUMAN
sp|O14737|PDCD5_HUMAN
sp|O14744|ANM5_HUMAN
sp|O14802|RPC1_HUMAN
sp|O14929|HAT1_HUMAN
sp|O14979|HNRDL_HUMAN
sp|O15020|SPTN2_HUMAN
sp|O15160|RPAC1_HUMAN
sp|O15213|WDR46_HUMAN
sp|O15235|RT12_HUMAN
sp|O15371|EIF3D_HUMAN
sp|O15372|EIF3H_HUMAN
sp|O43143|DHX15_HUMAN;sp|Q14562|DHX8_HUMAN
sp|O43172|PRP4_HUMAN
sp|O43390|HNRPR_HUMAN
sp|O43395|PRPF3_HUMAN
sp|O43491|E41L2_HUMAN;sp|Q9Y2J2|E41L3_HUMAN
sp|O43768|ENSA_HUMAN
sp|O43776|SYNC_HUMAN
sp|O43865|SAHH2_HUMAN;sp|Q96HN2|SAHH3_HUMAN

 

What information can I obtain and how ? can you please give me your opinion ?

Thanks

ADD COMMENTlink modified 5.0 years ago by Pierre Lindenbaum133k • written 5.0 years ago by Mo920
2

Your question is a bit vague. It is really helpful to tell us what you want to do, even if you don't know how to do it. What is the biological question you want to answer? Any background on experiment or previous analysis is also helpful.

ADD REPLYlink modified 13 months ago by _r_am32k • written 5.0 years ago by Sean Davis26k

@Sean Davis

all these proteins are from human. I would like to know for example what they share. or whether they are known or not. or I if I can find any information related to these proteins either seperatly or in a combination (interaction). Is there a way to make a map of sharing peptides etc.

ADD REPLYlink modified 13 months ago by _r_am32k • written 5.0 years ago by Mo920
5
gravatar for Pierre Lindenbaum
5.0 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum133k wrote:

A one-liner with http://string-db.org :

tr ";" "\n" < your-list.txt |\
cut -d '|' -f 3 |\
sort | uniq | tr "\n" "#" |\
sed 's/#/%0D/g' |\
xargs -I ID curl 'http://string-db.org/api/tsv-no-header/resolveList?identifiers=$ID' |\
cut -f 2 |\
tr "\n" "#" | sed 's/#/%0D/g'  |\
xargs -I ID curl -o output.png 'http://string-db.org/api/image/networkList?identifiers=$ID'

http://i.imgur.com/pL0SUY3

ADD COMMENTlink modified 13 months ago by _r_am32k • written 5.0 years ago by Pierre Lindenbaum133k

@Pierre Lindenbaum Nice, thanks !!!

ADD REPLYlink modified 13 months ago by _r_am32k • written 5.0 years ago by Mo920

@Pierre Lindenbaum I have tried to use a Mac terminal to get it run, the image is generated but i cannot open it. (I have tried to get different outputs format but still was the same) Do you have any idea where could be a problem? I think your syntax is for Linux ? I appreciate any comment

ADD REPLYlink modified 13 months ago by _r_am32k • written 5.0 years ago by Mo920

what the output of

file output.png
ADD REPLYlink modified 13 months ago by _r_am32k • written 5.0 years ago by Pierre Lindenbaum133k

I remove this to reduce the spam and make the question more clear

ADD REPLYlink modified 13 months ago by _r_am32k • written 5.0 years ago by Mo920
1

no this is the 'file' command http://linux.die.net/man/1/file

ADD REPLYlink written 5.0 years ago by Pierre Lindenbaum133k

opps!! It gave me this

file output.png
output.png: HTML document text
ADD REPLYlink modified 13 months ago by _r_am32k • written 5.0 years ago by Mo920

what is the content of the HTML ?...

ADD REPLYlink written 5.0 years ago by Pierre Lindenbaum133k

I tried to open it with different text editor, or image editor software. I cannot open it to know what is in there. You can download the output here http://wikisend.com/download/952744/output.png

ADD REPLYlink modified 13 months ago by _r_am32k • written 5.0 years ago by Mo920

`mv output.png output.html ` and try to open in a browser.

ADD REPLYlink written 5.0 years ago by Pierre Lindenbaum133k

Not Found

The requested URL /api/imag//networkList was not found on this server.


------- and with a text editor ------

<!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML 2.0//EN">
<html><head>
<title>404 Not Found</title>
</head><body>
<h1>Not Found</h1>
<p>The requested URL /api/imag//networkList was not found on this server.</p>
</body></html>
ADD REPLYlink modified 13 months ago by _r_am32k • written 5.0 years ago by Mo920

my bad when copy+paste. that was '/image' and not '/imag/' . I've fixed my code.

ADD REPLYlink written 5.0 years ago by Pierre Lindenbaum133k

Now I get the output as an image. Thanks it works now !!! one more question, your image is generated using entire list I pasted above or you select few of them? because I dont get the same trend as you showed above

ADD REPLYlink modified 13 months ago by _r_am32k • written 5.0 years ago by Mo920

I don't remember, I think that was the whole list.

ADD REPLYlink written 5.0 years ago by Pierre Lindenbaum133k

You might also consider using the web portal associated with String:

http://string-db.org/

ADD REPLYlink written 5.0 years ago by Sean Davis26k

@Pierre Lindenbaum how can I save the result as .SIF in order to load it to Cytoscape ? I will appreciate your comment

ADD REPLYlink modified 4.9 years ago • written 4.9 years ago by Mo920
1
gravatar for Sean Davis
5.0 years ago by
Sean Davis26k
National Institutes of Health, Bethesda, MD
Sean Davis26k wrote:

Well, there are many places to get information about proteins. To start, you might check:

https://en.wikipedia.org/wiki/List_of_biological_databases#Protein_sequence_databases

And for protein-protein interactions:

https://en.wikipedia.org/wiki/List_of_biological_databases#Protein-protein_and_other_molecular_interactions

The identifiers you have listed will generally be included in most of the databases on these lists. I guess it will be up to you to decide which is most useful to you based on what your needs are.

ADD COMMENTlink modified 13 months ago by _r_am32k • written 5.0 years ago by Sean Davis26k

@Sean Davis thanks although it is very general answer

ADD REPLYlink modified 13 months ago by _r_am32k • written 5.0 years ago by Mo920
1

Kind of a general question, too! Pierre read your mind, though, so hopefully you have what you need.

ADD REPLYlink modified 13 months ago by _r_am32k • written 5.0 years ago by Sean Davis26k
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