Turning genomics data into Biology课件.ppt

High level of conservation of co-regulation after speciation 76 % 精品文档 Comparing co-regulation in Bacteria indicates a level of conservation of 80% (operons in B. subtilis versus regulons in E.coli) NB: Based on operon conservation is only 50% Disregard cases of gene loss 精品文档 Noisy genomics data lead to drastic underestimations of conservation of interactions 精品文档 Conclusions co-regulation conservation Gene co-regulation tends to be conserved in Eukaryotes (76%) and in prokaryotes (80%) In the case of gene duplication one gene tends to maintain the co-regulatory link ? there appears to be one functionally equivalent ortholog Snel et al, Nucleic Acids Res 2004 精品文档 Turning genomics data into Biology Martijn Huynen Nijmegen Center for Molecular Life Sciences, Centre for Molecular and Biomolecular Informatics 精品文档 Comparative genomics Prediction of protein function, pathways The (somewhat) intelligent comparative genomics meat grinder Evolution of biosystems Method development 精品文档 A phosphomannomutase (pmm) is predicted to have acquired a phosphoribomutase (deoB) function deoD deoC deoA cdd pmm M.genitalium M.tuberculosis deoxyribose-1-P deoxycitidine deoxyuridine, deoxythimidine purine deoxyribonucleosides deoxyribose-5-P Glyceraldehyde-3-p, acetaldehyde Cdd DeoA DeoD deoC deoB deoB ? 精品文档 Predicting functional relations between genes using (conserved) genomic context Conserved Neighborhood Gene Fusion Co-occurrence Genomic Context Types: http://string.embl.de Snel et al., NAR 1999 von Mering et al., NAR 2002 von Mering et al, NAR 2005 Dandekar et al., 1998 Overbeek et al., 1999 Marcotte et al., 1999 Enright et al., 1999 Huynen and Bork 1998 Pellegrini et al., 1999 精品文档 PyrAB CarB MJ1378 MJ1381 MTH997 MTH996 EC0033 HP0919 AQ2101 AQ1172 AF1274 sll0370 Rv1384 YJL130C D2085.1 YJR109C 83 93 100 88 96 100 100 88 92 Gene fission in the evolution of carbamoyl phosphate synthase B (carB) 精品文档 Predicting functional interactions