I wish to find out all interactions WITHIN a set of around 200 HUMAN proteins. The identifiers I can use are genename, Uniprotaccession and Uniprot_Ids. So far I tried two plugins viz. MIMI and APID2NET.
MIMI doesn't seem to accept 200 proteins in one go, so I've to merge the networks. APID2NET shows too many nodes without any interactions. The STRING DB shows quite a many interactions for which MIMI/APID2NET don't report anything.
I tried the STRING plugin too, but it looks like it can accept one ID at a time. Am I missing something here?
Can somebody recommend some good and hassle less plugins/tricks to import PPIs. I've to do subsequently a BINGO analysis.
Thanks in advance
WoA
3 answers
You can look into BisoGenet plugin and it imports data from DIP, BIOGRID, HPRD, BIND, MINT and INTACT.
It also gives the GO, KEGG pathway information for each gene in the network. For each of the edges, it gives the database entry, the type of experiment and the corresponding PMIDs.
•
written
by
pixie@bioinfo
You may have a look at the Psicquic plugin : http://code.google.com/p/psicquic/wiki/CytoscapeClient
I didn't tried it myself but you should be able to query a list of protein and to search simultaneously all the psicquic provider databases.
Log in to answer this question.
-
Finding indel at end of contig with nucmer
written by kmyers2 •
-
Joining multiple query keys in entrez Efetch
written by timothy.kirkwood •
-
Tips to build a protein network
written by benoahb •
-
How To Resolve The Gene To Mrnas Relationships For The Human Genome?
written by Daniel Standage
-
On Retrieving Protein-Protein Interactions From String-Db
written by Woa
-
Best Way To Preprocess Barcoded Illumina Paired-End Data
written by Ying W
