Susanne Gerber, G. Hasenbrink, Wouter T. Hendriksen, P. van Heusden, J. Ludwig, E. Klipp, H. Lichtenberg-Fraté
{"title":"酿酒酵母PTRK1|2和PBMH1|2启动子区图谱分析及实验评价","authors":"Susanne Gerber, G. Hasenbrink, Wouter T. Hendriksen, P. van Heusden, J. Ludwig, E. Klipp, H. Lichtenberg-Fraté","doi":"10.1142/9781848165786_0002","DOIUrl":null,"url":null,"abstract":"We designed a simple graphical presentation for the results of a transcription factor (TF) pattern matching analysis. The TF analysis algorithm utilized known sequence signature motifs from several databases. The graphical presentation enabled a quick overview of potential TF binding sites, their frequency and spacing on both DNA strands and thus straight forward identification of promising candidates for further experimental investigations. The developed tool was applied on in total four Saccharomyces cerevisiae gene promoter regions. The selected differentially expressed genes belong to functionally different families and encode duplicate functions, TRK1 and TRK2 as ion transporters and BMH1 and BMH2 as multiple regulators. Output evaluation revealed a number of TFs with promising differences in the promoter regions of each gene pair. Experimental investigations were performed by using corresponding TF yeast mutants for either phenotypic analysis of ion transport mediated growth or expression analysis of BMH1,2 genes. Upon phenotypic testing one TF mutant exhibited severely impaired growth under non-permissive conditions. This TF, Mot3p was identified as of most abundant potential binding sites and distinctive patterns among the TRK promoter regions.","PeriodicalId":73143,"journal":{"name":"Genome informatics. International Conference on Genome Informatics","volume":"81 1","pages":"11-20"},"PeriodicalIF":0.0000,"publicationDate":"2010-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"1","resultStr":"{\"title\":\"Graphical analysis and experimental evaluation of Saccharomyces cerevisiae PTRK1|2 and PBMH1|2 promoter region.\",\"authors\":\"Susanne Gerber, G. Hasenbrink, Wouter T. Hendriksen, P. van Heusden, J. Ludwig, E. Klipp, H. Lichtenberg-Fraté\",\"doi\":\"10.1142/9781848165786_0002\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"We designed a simple graphical presentation for the results of a transcription factor (TF) pattern matching analysis. The TF analysis algorithm utilized known sequence signature motifs from several databases. The graphical presentation enabled a quick overview of potential TF binding sites, their frequency and spacing on both DNA strands and thus straight forward identification of promising candidates for further experimental investigations. The developed tool was applied on in total four Saccharomyces cerevisiae gene promoter regions. The selected differentially expressed genes belong to functionally different families and encode duplicate functions, TRK1 and TRK2 as ion transporters and BMH1 and BMH2 as multiple regulators. Output evaluation revealed a number of TFs with promising differences in the promoter regions of each gene pair. Experimental investigations were performed by using corresponding TF yeast mutants for either phenotypic analysis of ion transport mediated growth or expression analysis of BMH1,2 genes. Upon phenotypic testing one TF mutant exhibited severely impaired growth under non-permissive conditions. This TF, Mot3p was identified as of most abundant potential binding sites and distinctive patterns among the TRK promoter regions.\",\"PeriodicalId\":73143,\"journal\":{\"name\":\"Genome informatics. International Conference on Genome Informatics\",\"volume\":\"81 1\",\"pages\":\"11-20\"},\"PeriodicalIF\":0.0000,\"publicationDate\":\"2010-01-01\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"1\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Genome informatics. International Conference on Genome Informatics\",\"FirstCategoryId\":\"1085\",\"ListUrlMain\":\"https://doi.org/10.1142/9781848165786_0002\",\"RegionNum\":0,\"RegionCategory\":null,\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"\",\"JCRName\":\"\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Genome informatics. International Conference on Genome Informatics","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.1142/9781848165786_0002","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"","JCRName":"","Score":null,"Total":0}
Graphical analysis and experimental evaluation of Saccharomyces cerevisiae PTRK1|2 and PBMH1|2 promoter region.
We designed a simple graphical presentation for the results of a transcription factor (TF) pattern matching analysis. The TF analysis algorithm utilized known sequence signature motifs from several databases. The graphical presentation enabled a quick overview of potential TF binding sites, their frequency and spacing on both DNA strands and thus straight forward identification of promising candidates for further experimental investigations. The developed tool was applied on in total four Saccharomyces cerevisiae gene promoter regions. The selected differentially expressed genes belong to functionally different families and encode duplicate functions, TRK1 and TRK2 as ion transporters and BMH1 and BMH2 as multiple regulators. Output evaluation revealed a number of TFs with promising differences in the promoter regions of each gene pair. Experimental investigations were performed by using corresponding TF yeast mutants for either phenotypic analysis of ion transport mediated growth or expression analysis of BMH1,2 genes. Upon phenotypic testing one TF mutant exhibited severely impaired growth under non-permissive conditions. This TF, Mot3p was identified as of most abundant potential binding sites and distinctive patterns among the TRK promoter regions.