[Bioperl-l] Re: [RFC] Interolog::Walk

Siddhartha Basu sidd.basu at gmail.com
Wed Aug 18 20:28:32 EDT 2010


On Wed, 18 Aug 2010, Giuseppe Gallone wrote:

> Hello BioPerl community - I've written a new module called Interolog::Walk 
> that I'm planning to put on CPAN. I would be grateful if you might take a 
> look at the brief description I attached and tell me what you think. I'll 
> be more than happy to post further details should the module be of some 
> interest for someone.
> Also, I am not totally sure about having the correct name for it. This is 
> my first module and It would be great if you could advise on naming it 
> appropriately. Hopefully the following description will give an idea on 
> what it does.
> ===================
>     Interolog::Walk - Retrieve, score and visualize putative 
> Protein-Protein Interactions through the orthology-walk method
>     A common activity in computational biology is to mine protein-protein 
> interactions from publicly available databases in order to build 
> Protein-Protein Interaction (PPI) datasets.
> In many instances, however, the number of experimentally obtained annotated 
> PPIs is very scarce and it would be helpful to enrich the experimental 
> dataset with high-quality, computationally-inferred PPIs. Such 
> computationally-obtained dataset can extend, support or enrich experimental 
> PPI datasets, and are of crucial importance in high-throughput gene 
> prioritization studies, i.e. to drive hypotheses and restrict the 
> dimensionality of many gene functional discovery problems.
> This Perl Module, Interolog::Walk, is aimed at building putative PPI 
> datasets on the basis of a number of comparative biology paradigms: the 
> module implements a collection of computational biology algorithms based on 
> the concept of "orthology projection". If interacting proteins A and B in 
> organism X have orthologs A' and B' in organism Y, under certain conditions 
> one can assume that the interaction will be conserved in organism Y, i.e. 
> the A-B interaction can be "projected through the orthologies" to obtain a 
> putative A'-B' interaction. The pair of interactions (A-B) and (A'-B') are 
> named "Interologs" (see for instance [1] and [2]).
> Interolog::Walk collects, analyses and collates gene orthology data 
> provided by the Ensembl Consortium (www.ensembl.org) as well as PPI data 
> provided by EBI Intact (http://www.ebi.ac.uk/intact/). It provides the user 
> with the possibility of rating the quality and reliability of the putative 
> interactions collected, by means of confidence scores, and optionally 
> outputs network representations of the datasets, compatible with the 
> biological network representation standard, Cytoscape.

Sounds interesting. I am currently playing around with a perl based webapp for displaying interactome
using cytoscapeweb. Depending how your design pans out,  would be happy to
use your module as a backend analysis layer. And on a related note,  you
might want to have a look at bioperl-network and if there is any overlap
might be worth contributing.


> In order to carry out an interolog walk we start with a set of gene 
> identifiers in one organism of interest. We query those ids against a 
> number of comparative biology databases to retrieve a list of orthologues 
> for each gene id of interest, in one or more species.
> In the following step we rely  on PPI databases to retrieve the list of 
> available interactors for the protein ids obtained. The output at this 
> stage consists of a list of interactors of the orthologues of the initial 
> gene set, plus several fields of ancillary data.
> In the last step of the process we  project the interactions - again using 
> orthology data - back to the original species of interest. The output of 
> the process is a list of PUTATIVE INTERACTORS of the initial gene set, plus 
> several fields of ancillary data.
> ====================
> Given the scope and the focus of the project, I would imagine that viable 
> alternatives for the namespace might be
> Bio::Orthology::InterologWalk
> Bio::InterologMap
> or maybe
> Interolog::Map
> Orthology::Map
> Orthology::InterologMap
> There are no similar projects as far as I could see so I shouldn't run the 
> risk of overlapping namespaces. Still I would love to know your informed 
> opinion about it.
> best,
> Giuseppe
> [1] Yu H, Luscombe NM, Lu HX, Zhu X, Xia Y, Han JD, Bertin N, Chung S, 
> Vidal M, Gerstein M. Annotation transfer between genomes: protein-protein 
> interologs and protein-DNA regulogs. Genome Research 2004 
> Jun;14(6):1107-18.
> [2]Wiles AM, Doderer M, Ruan J, Gu T-T, Ravi D, Blackman BA, Bishop AJR. 
> "Building and Analyzing Protein Interactome Networks by Cross-species 
> Comparisons." BMC Systems Biology 2010, 4:36 - PMID: 20353594
> -- 
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> Scotland, with registration number SC005336.
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