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.
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.
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
As far as I know HPRD hasn't been updated since 2010 so its data is outdated.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.
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!
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 ??!!
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.
@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 ?
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version 2.3.6
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.
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.
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.