How can I integrate gene with PPI network

Question

[AAhmed]

I have microarray datasets, I did statistical analysis to it and I got 75 significant genes. I want to map these genes on PPI network to find out their interaction. Therefore, I download IntAct PPI network. I am new in this field and I do not have clue how to map genes on PPI. Do I have to convert these genes to protein or what? any help will be highly appreciated

Answer 1

[Tom_L]

You can use the bioconductor package "STRINGdb", assuming you're a little comfortable using R programming language. Basically, you can obtain your PPI network with 3 commands:

string_db=STRINGdb$new(version="10",species=9606,score_threshold=400,input_directory="YOUR_PATH")

myDF=string_db$map(myDF,"GENE_NAME",removeUnmappedRows=TRUE)

string_db$plot_network(myDF$STRING_id,n=200)

The first line generates a STRINGdb object containing some parameters for further computation (e.g. specie, PPI score threshold, etc.).

The second line takes a data frame (myDF) in input and converts column "GENE_NAME" containing gene symbols into a new column called "STRING_id". Note that "removeUnmappedRows=TRUE" will remove unknown gene symbols.

The third line plots your network using the new column with STRINGdb entries.

Some additional documentation: https://bioconductor.org/packages/release/bioc/vignettes/STRINGdb/inst/doc/STRINGdb.pdf

Cheers.

[AAhmed]

Thank you for your help Tom_L This really helpful

[AAhmed]

Can I used R to import the network from Human Protein Reference Database(HPRD) rather then STRING? @Tom_L

Answer 2

[Girolamo]

I suggest to convert your list to uniprot id:

• cut and paste you list here http://www.uniprot.org/uploadlists/
• select Entrez Gene to uniprotKB
• download the list of targets
• upload the list of targets here http://www.ebi.ac.uk/intact/

Answer 3

[Girolamo]

what kind of id you have for your genes? you can directly upload your ids here http://www.ebi.ac.uk/intact/ and retrieve the interactions. Alternatively, you could use http://www.uniprot.org/uploadlists/ to retrieve the mapping genes-proteins

Answer 4

[AAhmed]

I have Gene_Entrez and Gene_Symbols. Could you explain this a little bit how can I know my genes in this case if I used http://www.ebi.ac.uk/intact/ or http://www.uniprot.org/uploadlists/

Answer 5

[Ron]

https://thebiogrid.org/download.php

"BioGRID is an interaction repository with data compiled through comprehensive curation efforts. Our current index is version 3.4.142 and searches 57,513 publications for 1,079,789 protein and genetic interactions, 27,745 chemical associations and 38,559 post translational modifications from major model organism species. "