Interspecies translation

See the Coming soon section

All the conclusions extracted by SIMScells are based in human biological systems. However, it is possible to do an extrapolation of the results obtained from questioning the models to different species by conducting a homology study of the proteins involved.

Two genes/proteins are homologous when they are related by common ancestry. It also implies that the genes are likely to share the same function or activity. This type of homologous relationship is characteristic of orthologs, genes/proteins that are related through a speciation event. I.e Orthologs have homologous origin and are likely to have similar functions/activities. There are many algorithms/databases that have compiled sets of orthologous groups for whole genomes. They almost all begin with a Best Reciprocal Hit approach (explained below) and most use additional methods such as synteny, phylogenetic reconstruction and/or manual annotation to increase the confidence in their orthology assignments.

SIMScells uses two sources for assessing the homology between two proteins:

  •  An algorithm called INPARANOID and the derived database, Inparanoid, which contains a collection of pairwise ortholog groups between the most important experimental species.
  •  Best Reciprocal Hit method using the public tool called BLAST (BLAST. Basic Local Alignment Search Tool. [Available from: http://blast.ncbi.nlm.nih.gov/] for assessing the homology between two proteins.

If all the human proteins involved in the answer to the question made to the model have an ortholog in the species of interest, then the answer can be extrapolated to this species.