Question: How can I integrate gene with PPI network
2
gravatar for AAhmed
2.9 years ago by
AAhmed20
AAhmed20 wrote:

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

gene • 2.4k views
ADD COMMENTlink modified 2.3 years ago by Ron910 • written 2.9 years ago by AAhmed20
5
gravatar for Tom_L
2.3 years ago by
Tom_L310
Tom_L310 wrote:

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.

ADD COMMENTlink written 2.3 years ago by Tom_L310

Thank you for your help Tom_L This really helpful

ADD REPLYlink written 2.0 years ago by AAhmed20

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

ADD REPLYlink modified 2.0 years ago • written 2.0 years ago by AAhmed20
1
gravatar for Girolamo
2.9 years ago by
Girolamo140
Italia
Girolamo140 wrote:

I suggest to convert your list to uniprot id:

ADD COMMENTlink written 2.9 years ago by Girolamo140
0
gravatar for Girolamo
2.9 years ago by
Girolamo140
Italia
Girolamo140 wrote:

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

ADD COMMENTlink written 2.9 years ago by Girolamo140
0
gravatar for AAhmed
2.9 years ago by
AAhmed20
AAhmed20 wrote:

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/

ADD COMMENTlink written 2.9 years ago by AAhmed20
0
gravatar for Ron
2.3 years ago by
Ron910
United States
Ron910 wrote:

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. "

ADD COMMENTlink written 2.3 years ago by Ron910
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