For Generating PPI

Question

[NS]

Dear all, I am extremely new to the "omics" world and am trying to analyse some big RNA seq data. I wanted to know how to generate PPI for a set of human genes that I have. 1) Can I directly feed the list on to STRING data base and key in the parameters such as set to a string score of 0.7 and retrieve the PPI? 2) Do I need to blast the genes and only select those with a predetermined E value to feed into STRING? If so, can I blast all my genes at one go? (I am unaware of how to blast the genes and the parameters to set) I am extremely new to this and hence asking and thoroughly confused.

Kindly help.

Thank you.

[Martombo]

Why would you blast your gene sequences? STRING database has got human-specific entries. You can download the whole network from their website.

[karthic]

Have you assembled your RNAseq raw data and identified the unigenes?? If so, you can download the string db, make a local blast db in your computer and blast those unigenes against the string db. This way you get the string ids and you can verify those strings by searching them in the interaction table available at the string website itself. below is the sample command to run blast,

blastx -query transcripts.fasta -db string_protein.sequences.v10.5.fa.00 -num_threads 25 -outfmt 6 -num_alignments 1 -evalue 0.00001 -out /blastx_string_output

KK