<p>I realized that some tools work better with Gene Names instead of some type of ID.</p>

<p>Using IIS I was capable of creating a network using <a href="http://www.uniprot.org/uniprot/?query=streptomyces+caatingaensis&amp;sort=score" rel="nofollow noreferrer">this list</a> of proteins (<em>Streptomyces caatingaensis</em>) by querying proteins by Genes Names having as base the E. Coli.</p>

<p>The tool has 3 main tabs: proteins, annotation, and interactome.
Search the Gene Names in proteins section, go to Interactome, set the parameters and create the network.</p>

<p>P.S. If you are not used to the tool you should read the research article available on the home page before using the network for research purposes.</p>

CC BY-SA 3.0
2017-11-15T01:09:10.590Z
2017-11-15T01:18:49.953Z
2017-11-15T01:18:49.953Z
Henry
<p>I have a list of gene/protein IDs and I could not query a network using String, BioGrid, Intact and IIS, for Streptomyces thioluteus.</p>

<p>The bacteria I am working with is the <em>Streptomyces caatingaensis</em>. Since it is newer than others, I thought I would find an interaction network looking for <em>Streptomyces thioluteus</em> (which shares one pathway I am analyzing in common, others do not share). As a result, I have <a href="http://www.uniprot.org/uniprot/?query=streptomyces%20thioluteus&amp;sort=score" rel="nofollow noreferrer">this list</a> of proteins, but I could not query any network from the IDs. Sometimes I could not find the bacterium in the tools and when it was found, as in <a href="http://bioinfo03.ibi.unicamp.br/lnbio/IIS2/" rel="nofollow noreferrer">IIS</a> the result was <strong>zero</strong> interactions.</p>

<p>Is there anything I could use to have some network that could be used as insight for the analysis?</p>

<database><proteins><networks>
How to query a network for a bacterium, specifically Streptomyces caatingaensis or Streptomyces thioluteus?
# How to query a network for a bacterium, specifically Streptomyces caatingaensis or Streptomyces thioluteus?

(Asked by: username_0 on 2017-11-11)

I have a list of gene/protein IDs and I could not query a network using String, BioGrid, Intact and IIS, for Streptomyces thioluteus.

The bacteria I am working with is the *Streptomyces caatingaensis*. Since it is newer than others, I thought I would find an interaction network looking for *Streptomyces thioluteus* (which shares one pathway I am analyzing in common, others do not share). As a result, I have [this list](http://www.uniprot.org/uniprot/?query=streptomyces%20thioluteus&sort=score) of proteins, but I could not query any network from the IDs. Sometimes I could not find the bacterium in the tools and when it was found, as in [IIS](http://bioinfo03.ibi.unicamp.br/lnbio/IIS2/) the result was **zero** interactions.

Is there anything I could use to have some network that could be used as insight for the analysis?

**Tags:** database, proteins, networks

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## 1 answers

### Answer by username_0 on 2017-11-15. Score: 1 | Accepted answer

I realized that some tools work better with Gene Names instead of some type of ID.

Using IIS I was capable of creating a network using [this list](http://www.uniprot.org/uniprot/?query=streptomyces+caatingaensis&sort=score) of proteins (*Streptomyces caatingaensis*) by querying proteins by Genes Names having as base the E. Coli.

The tool has 3 main tabs: proteins, annotation, and interactome.
Search the Gene Names in proteins section, go to Interactome, set the parameters and create the network.

P.S. If you are not used to the tool you should read the research article available on the home page before using the network for research purposes.


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