Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs. Export

@article{citeulike:227096, abstract = {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 an online database at http://interolog.gersteinlab.org. Specifically, we are able to transfer approximately 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.}, address = {Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA.}, author = {Yu, Haiyuan and Luscombe, Nicholas M. and Lu, Hao Xin X. and Zhu, Xiaowei and Xia, Yu and Han, Jing-Dong D. and Bertin, Nicolas and Chung, Sambath and Vidal, Marc and Gerstein, Mark}, citeulike-article-id = {227096}, citeulike-linkout-0 = {http://dx.doi.org/10.1101/gr.1774904}, citeulike-linkout-1 = {http://genome.cshlp.org/content/14/6/1107.abstract}, citeulike-linkout-2 = {http://genome.cshlp.org/content/14/6/1107.full.pdf}, citeulike-linkout-3 = {http://www.genome.org/cgi/content/abstract/14/6/1107}, citeulike-linkout-4 = {http://view.ncbi.nlm.nih.gov/pubmed/15173116}, citeulike-linkout-5 = {http://www.hubmed.org/display.cgi?uids=15173116}, citeulike-linkout-6 = {http://www.wormbase.org/db/misc/paper?name=WBPaper00013476}, doi = {10.1101/gr.1774904}, issn = {1088-9051}, journal = {Genome research}, keywords = {interolog, ppi}, month = {June}, number = {6}, pages = {1107--1118}, posted-at = {2009-07-08 08:04:36}, priority = {2}, title = {Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs.}, url = {http://dx.doi.org/10.1101/gr.1774904}, volume = {14}, year = {2004} }

TY - JOUR ID - citeulike:227096 L3 - citeulike-article-id:227096 N2 - 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 an online database at http://interolog.gersteinlab.org. Specifically, we are able to transfer approximately 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. IS - 6 JF - Genome research SN - 1088-9051 AD - Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA. EP - 1118 TI - Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs. VL - 14 SP - 1107 KW - interolog KW - ppi AU - Yu, Haiyuan AU - Luscombe, Nicholas AU - Lu, Hao Xin AU - Zhu, Xiaowei AU - Xia, Yu AU - Han, Jing-Dong AU - Bertin, Nicolas AU - Chung, Sambath AU - Vidal, Marc AU - Gerstein, Mark PY - 2004/06// UR - http://dx.doi.org/10.1101/gr.1774904 ER -