<p>I am new to string analyses (and to python), and I have 2 questions. I need to identify couples of proteins from an input list that are interacting together. I tried the following :</p>
<p>1 - Downloading the protein full network data for humans from the String website (wget <a href="https://stringdb-downloads.org/download/protein.links.v12.0.txt.gz" rel="nofollow noreferrer">https://stringdb-downloads.org/download/protein.links.v12.0.txt.gz</a>), which gives me a file looking like this, with ensembl ID for humans preceded by the human species prefix (9606) :</p>
<pre><code>                      protein1              protein2  combined_score
0         9606.ENSP00000000233  9606.ENSP00000356607             173
1         9606.ENSP00000000233  9606.ENSP00000427567             154
2         9606.ENSP00000000233  9606.ENSP00000253413             151
3         9606.ENSP00000000233  9606.ENSP00000493357             471
</code></pre>
<p>2 - Identifying couples of proteins present in my list :</p>
<pre><code>import pandas as pd
ppi_data=pd.read_csv(&quot;9606.protein.links.v12.0.txt.gz&quot;, sep = &quot; &quot;)
protein_list = [&quot;9606.ENSP00000357927&quot;, &quot;9606.ENSP00000360411&quot;, &quot;9606.ENSP00000346643&quot;]
filtered_ppi = ppi_data(ppi_data[&quot;protein1&quot;].isin(protein_list)) &amp; (ppi_data[&quot;protein2&quot;].isin(protein_list))]
</code></pre>
<p>This seemed to work, and I retrieved an output with couples of proteins. To check the absence of error I searched for the identifiers in the String website. Here is my first question : the String website does not seem to recognize the ensembl ID. It doesn't work with the normal ID (ENSP00000265080 format), nor with the ID preceded by the specie prefix (9606.ENSP00000265080). Does anyone know why ?</p>
<p>Here is my second question : I found on uniprot the protein names corresponding to 2 of my ensembl ID (RASGRF2 pour 9606.ENSP00000265080 and HKDC1 pour 9606.ENSP00000346643), and I searched them on the string website using the &quot;multiple proteins&quot; option. However, the website did not found any interaction between these proteins (see below). Does anyone know why ?</p>
<p><a href="https://i.sstatic.net/Th9hzgJj.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/Th9hzgJj.png" alt="enter image description here" /></a>
<a href="https://string-db.org/cgi/network?taskId=bwdNkTpOcVLe&amp;sessionId=b1np2TuNijFp" rel="nofollow noreferrer">https://string-db.org/cgi/network?taskId=bwdNkTpOcVLe&amp;sessionId=b1np2TuNijFp</a></p>
<p>Thank you very much for your help !</p>
<p>Lily</p>

CC BY-SA 4.0
2024-12-06T15:24:43.200Z
Do you know that RASGRF2 and HKDC1 interact?
terdon
CC BY-SA 4.0
2024-12-09T07:39:20.303Z
I do not know @terdon, I do not usually work on these proteins. They are not indicated as interacting together in uniprot, biogrid (https://thebiogrid.org/111859) or intact (https://www.ebi.ac.uk/intact/search?query=id:O14827*&layout=cise#interactor). It's possible I misinterpretated the data, but how should I read the output I got in Python ?
Lily
<ensembl><protein-protein-interaction><stringdb>
Identify interactions between proteins of interest
# Identify interactions between proteins of interest

(Asked by: username_0 on 2024-12-05)

I am new to string analyses (and to python), and I have 2 questions. I need to identify couples of proteins from an input list that are interacting together. I tried the following :
1 - Downloading the protein full network data for humans from the String website (wget https://stringdb-downloads.org/download/protein.links.v12.0.txt.gz), which gives me a file looking like this, with ensembl ID for humans preceded by the human species prefix (9606) :
                      protein1              protein2  combined_score
0         9606.ENSP00000000233  9606.ENSP00000356607             173
1         9606.ENSP00000000233  9606.ENSP00000427567             154
2         9606.ENSP00000000233  9606.ENSP00000253413             151
3         9606.ENSP00000000233  9606.ENSP00000493357             471

2 - Identifying couples of proteins present in my list :
import pandas as pd
ppi_data=pd.read_csv("9606.protein.links.v12.0.txt.gz", sep = " ")
protein_list = ["9606.ENSP00000357927", "9606.ENSP00000360411", "9606.ENSP00000346643"]
filtered_ppi = ppi_data(ppi_data["protein1"].isin(protein_list)) & (ppi_data["protein2"].isin(protein_list))]

This seemed to work, and I retrieved an output with couples of proteins. To check the absence of error I searched for the identifiers in the String website. Here is my first question : the String website does not seem to recognize the ensembl ID. It doesn't work with the normal ID (ENSP00000265080 format), nor with the ID preceded by the specie prefix (9606.ENSP00000265080). Does anyone know why ?
Here is my second question : I found on uniprot the protein names corresponding to 2 of my ensembl ID (RASGRF2 pour 9606.ENSP00000265080 and HKDC1 pour 9606.ENSP00000346643), and I searched them on the string website using the "multiple proteins" option. However, the website did not found any interaction between these proteins (see below). Does anyone know why ?

https://string-db.org/cgi/network?taskId=bwdNkTpOcVLe&sessionId=b1np2TuNijFp
Thank you very much for your help !
Lily

**Tags:** ensembl, protein-protein-interaction, stringdb
> **Comments:**
> **username_1**: Do you know that RASGRF2 and HKDC1 interact?  
> **username_0**: I do not know @terdon, I do not usually work on these proteins. They are not indicated as interacting together in uniprot, biogrid (https://thebiogrid.org/111859) or intact (https://www.ebi.ac.uk/intact/search?query=id:O14827*&layout=cise#interactor). It's possible I misinterpretated the data, but how should I read the output I got in Python ?  

---

## 0 answers

