Let's say I have a list of proteins ID. I would like to know whether I can find any complex based on that list. Any example, explanation is appreciated.

An example input is what you see below. What can I do with the following list of protein IDs? These IDs are from human.

P41182,P56524, P41182,Q9UQL6, P41182,Q8WUI4,Q92793,Q09472,Q9Y6Q9,Q92831
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    $\begingroup$ Could you clarify what you mean by "complex"? Do you want to know if they are part of an oligomeric quaternary structure, or how they interact with other proteins? $\endgroup$ – James Feb 26 '16 at 3:35
  • $\begingroup$ @James if they are part of oligomeric quaternary structure $\endgroup$ – Nik Feb 26 '16 at 8:27
  • $\begingroup$ This question is not a homework question. It is not a trivial, easily google-able task. I buy the "too-broad" argument, but closing this for homework seems a bit naive. Even if it's an assignment it's a tough one if you don't know where to start! $\endgroup$ – James Mar 3 '16 at 2:55
  • $\begingroup$ Without a pairwise mapping between interacting proteins, you cannot make the network. Do you have a file that contains this information? $\endgroup$ – WYSIWYG Mar 3 '16 at 6:59
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    $\begingroup$ @Mol no you cannot assume so. In a protein extract from a eukaryotic cell actin and cyclin would both be present but they do not interact. $\endgroup$ – WYSIWYG Mar 3 '16 at 18:46

This is not a trivial task depending on how well studied your network is or what information you want to gather. It sounds like an interaction dataset is what you want rather than scouring the PDB for static structures (that would be such a hit and miss process I'm not sure it's worth bothering).

  1. Upload you list of gene codes to string-db.

    • You'll see the network here, and structures are made clear of known complexes in an expandable thumbnail.
    • It's a limited web-server tool, and whilst very powerful, isn't very flexible. Cytoscape might be needed for a more novel study because it is scriptable.

    You can probably stop here and investigate your network.

  2. From string-db download the .txt file (TXT - simple tab delimited flatfile). I think it's an old-school save icon on the web-server, although if you're uploading multiple identifiers, it is simply the "save" button at the top left.

  3. Download Cytoscape here.

  4. Then use File>Import>Table>From file.
  5. This will build an interaction network and you'll see which genes/proteins interact with one another.

Catch: whilst this provides spacial information, you can't get a picture of temporal information: i.e you know what is interacting, but not when nor for how long.

  • $\begingroup$ how to get the .SIF ? how to give all the ID together ? i tried to save it but it did not give me any .SIF $\endgroup$ – Nik Feb 29 '16 at 16:29
  • $\begingroup$ Did you manage to get string-db to display an interaction network? $\endgroup$ – James Mar 1 '16 at 1:50
  • $\begingroup$ not for all IDs together but when I use one ID, it works $\endgroup$ – Nik Mar 1 '16 at 7:23
  • $\begingroup$ Have you tried uploading them all at once under the multiple identifiers tab? $\endgroup$ – James Mar 1 '16 at 7:30
  • $\begingroup$ both txt files are the same ? also can you please give me some hint related to the CytoScape? what to study and where to study so that I can get an idea how to build the network and visualise it $\endgroup$ – Nik Mar 1 '16 at 11:34

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