Annotation transfer between genomes : Protein-protein interrologs and protein-DNA regulogs

Research output: Journal Publications and ReviewsRGC 21 - Publication in refereed journalpeer-review

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  • Haiyuan Yu
  • Nicholas M. Luscombe
  • Hao Xin Lu
  • Yu Xia
  • Jing-Dong J. Han
  • Nicolas Bertin
  • Sambath Chung
  • Marc Vidal
  • Mark Gerstein


Original languageEnglish
Pages (from-to)1107-1118
Journal / PublicationGenome Research
Issue number6
Publication statusPublished - Jun 2004
Externally publishedYes


Proteins function mainly through interactions, especially with DNA and other proteins. While some large-scale interaction networks are now available for a number of model organisms, their experimental generation remains difficult. Consequently, interolog mapping - the transfer of interaction annotation from one organism to another using comparative genomics - is of significant value. Here we quantitatively assess the degree to which interologs can be reliably transferred between species as a function of the sequence similarity of the corresponding interacting proteins. Using interaction information from Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, and Helicobacter pylori, we find that protein-protein interactions can be transferred when a pair of proteins has a joint sequence identity > 80% or a joint E-value <10-70. (These "joint" quantities are the geometric means of the identities or E-values for the two pairs of interacting proteins.) We generalize our interolog analysis to protein-DNA binding, finding such interactions are conserved at specific thresholds between 30% and 60% sequence identity depending on the protein family. Furthermore, we introduce the concept of a " regulog" - a conserved regulatory relationship between proteins across different species. We map interologs and regulogs from yeast to a number of genomes with limited experimental annotation (e.g., Arabidopsis thaliana) and make these available through all online database at Specifically, we are able to transfer ∼90,000 potential protein-protein interactions to the worm. We test a number of these in two-hybrid experiments and are able to verify 45 overlaps, which we show to be statistically significant. ©2004 by Cold Spring Harbor Laboratory Press.

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Citation Format(s)

Annotation transfer between genomes: Protein-protein interrologs and protein-DNA regulogs. / Yu, Haiyuan; Luscombe, Nicholas M.; Lu, Hao Xin et al.
In: Genome Research, Vol. 14, No. 6, 06.2004, p. 1107-1118.

Research output: Journal Publications and ReviewsRGC 21 - Publication in refereed journalpeer-review