[Bioperl-l] Re: [RFC] Interolog::Walk
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  and ).
> 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
> or maybe
> 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.
>  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
> 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
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.
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