Qualitative analysis of context based PPI prediction

Question

[benjaminoelke]

So hello everybody,

I am a bachelor student of bioinformatics and for my thesis I have to do a qualitative analysis of context based ppi prediction in String DB. I have so far extracted a subset of PPI's that involve proteins that are included in SwissProt and to test my method (which I will still have to develop ) I have taken all Human PPI from that subset. (around 8 milion interactions)

I now need some advice for a dataset to test the String predictions against and I am a litle bit overwhelmed with the myriad of available PPI data. Furthermore there doesn't seem to be a comprehensive database as most datasets I could find focus on specialised aspects of PPI's I'd like to take the interaction data from UniProt however I might be too unskilled to find the proper download options or files.

Anyone has any ideas that might help me ?

Cheers

Answer 1

[natasha.sernova]

See the following articles and tool-descriptions:

InPrePPI looks especially useful.

InPrePPI: an integrated evaluation method based on genomic context for predicting protein-protein interactions in prokaryotic genomes

http://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-8-414

Evaluation of Physical and Functional Protein-Protein Interaction Prediction Methods for Detecting Biological Pathways

http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0054325

Construction and analysis of protein–protein interaction networks

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2834675/

PinSnps: structural and functional analysis of SNPs in the context of protein interaction networks

http://bioinformatics.oxfordjournals.org/content/early/2016/05/18/bioinformatics.btw153.full

Many PPI-prediction software tools:

https://omictools.com/protein-protein-interaction-prediction-category

Answer 2

[benjaminoelke]

thx

I am already using many ideas from InPrePPI but the other links seem promising