Question: how to link list of genes using PPI networks?
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gravatar for Chaimaa
22 months ago by
Chaimaa150
Chaimaa150 wrote:

hi guys i have a list of disease genes, and i want to use any PPI networks like HPRD or HumanNet to link these genes I appreciate any help plz ! Note that I want to implement his idea in MATLAB.

disease genes ppi networks • 959 views
ADD COMMENTlink modified 21 months ago by Jean-Karim Heriche18k • written 22 months ago by Chaimaa150
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StringDB online tool: http://string-db.org/

StringDB R-package: http://bioconductor.org/packages/release/bioc/html/STRINGdb.html

Takes a list of genes as input to plot PPI network based on selected parameters.

ADD REPLYlink modified 22 months ago • written 22 months ago by YaGalbi1.4k

Thanks, bro I will try your tool which you share with me, and if you have any idea about how to use HPRD to link or connect those genes i will be too happy to know. As i have got HPRD release 9 but i don't know how to deal with it to connect my genes.

ADD REPLYlink written 21 months ago by Chaimaa150

Thanks, bro I will try your tool which you share with me, and if you have any idea about how to use HPRD to link or connect those genes i will be too happy to know. As i have got HPRD release 9 but i don't know how to deal with it to connect my genes.

ADD REPLYlink written 21 months ago by Chaimaa150
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gravatar for Jean-Karim Heriche
21 months ago by
EMBL Heidelberg, Germany
Jean-Karim Heriche18k wrote:

As data sources, you can use any number of public databases containing human protein-protein interactions. For a more exhaustive graph of interactions, you could use iRefIndex which combines interactions from several databases. As for the Matlab part, Matlab is not very much used in bioinformatics so there may not be ready-to-use tools for dealing with protein-protein interactions. If Matlab has tools for dealing with graphs, you could try using them and see how far they get you. Otherwise, I think you'll have to code how to extract the interactions you want yourself.

ADD COMMENTlink written 21 months ago by Jean-Karim Heriche18k

Thanks bro, and if you have any idea about how to use HPRD or HumanNet databases to link these genes plz share with me .now i have 2 textfiles :HPRD (BINARY_PROTEIN_PROTEIN_INTERACTIONS.txt) and my textfile (genes.txt) and i'm struggling to link and connect my genes using HPRD network

ADD REPLYlink written 21 months ago by Chaimaa150
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As far as I know HPRD hasn't been updated since 2010 so its data is outdated. I would advise you to use a more up-to-date data source. Anyway, the resources (including HPRD) usually provide the interactions in tab-delimited format with one interaction per line. Building your network is simply a matter of extracting the relevant lines. If you're interested only in interactions between your genes of interest then simply extract the lines where both interaction partners are in your list of genes.

ADD REPLYlink modified 21 months ago • written 21 months ago by Jean-Karim Heriche18k

yes i agree with you but my goal is to try different PPIs and check which one can prouduce sparce network in case of HPRD: i already get HPRD textfile (BINARY_PROTEIN_PROTEIN_INTERACTIONS.txt) which have 39240 interactions (including self interactions) and my textfile have 200 genes . So do i need to extract the interactions between these 200 genes based on HPRD manullay or programmatically ? could you explain for me how to do that if you don't mind ? i really appreciate your help!

ADD REPLYlink written 21 months ago by Chaimaa150
1

Given that you need to go through ~39000 lines to look for any of ~20000 possible interactions between your 200 genes, which way do you think is best ? I'll leave the rest as an exercise, I think it would be good for you if you spent the time thinking about it.

ADD REPLYlink written 21 months ago by Jean-Karim Heriche18k

Definitely, I have to do it programmatically As i'm using MATLAB and so i have to compare the HPRD textfile with my gene_list text file and whenever i find the gene of interest wich exist in my file in the HPRD textfile do will save the correponding line(means interaction) till end of file i'm right ??!!

ADD REPLYlink modified 21 months ago • written 21 months ago by Chaimaa150
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Yes if you want all interactions involving one of your genes but remember that because each line is an interaction, it will have two genes so if you want interactions only between your genes, you have to make sure that both members of the interaction are in your list.

ADD REPLYlink written 21 months ago by Jean-Karim Heriche18k

@Jean-Karim Heriche Thank you too much bro ! i will take your comments into consideration. Last question i want to ask you: is there a way to do this job by some tools like to import both textfiles and merge them and then highlight genes of interest with their edges, is it possible ?

ADD REPLYlink written 21 months ago by Chaimaa150
1

I don't think there's any ready-to-use tool to do what you want but even if there were, it is a relatively simple scripting task that is so common in bioinformatics in one form or another that it would be good if you learned how to do it.

ADD REPLYlink written 21 months ago by Jean-Karim Heriche18k

Thanks @Jean-Karim Heriche

ADD REPLYlink written 21 months ago by Chaimaa150
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