{"title":"Setting CAGE Tags in a Genomic Context","authors":"G. Faulkner, S. Grimmond","doi":"10.4032/9789814241359","DOIUrl":"https://doi.org/10.4032/9789814241359","url":null,"abstract":"The detection and quantification of transcriptional activity on the genome by CAGE requires reliable and high-throughput tag mapping. Here, we discuss the basic considerations of sequence tag mapping and how these apply to CAGE. The current CAGE mapping pipeline is then described in detail, in particular how it has been updated to utilize iterative global exact matching for each tag rather than heuristic algorithm local alignment. Combined with the addition of a novel method to resolve tags that map to multiple genomic locations, the most recent evolution of the CAGE mapping pipeline is faster, more accurate and provides better coverage than the previous approach, as we demonstrate using a sample CAGE library. Finally, the pipeline is easily customized for other sequence tag technologies, suggesting broad utility in the era of next-generation sequencing.","PeriodicalId":182337,"journal":{"name":"Cap-Analysis Gene Expression (Cage)","volume":"70 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2019-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"123445646","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Using CAGE Data for Quantitative Expression","authors":"M. Hoon, N. Bertin, A. Chalk","doi":"10.1201/9780429065750-9","DOIUrl":"https://doi.org/10.1201/9780429065750-9","url":null,"abstract":"","PeriodicalId":182337,"journal":{"name":"Cap-Analysis Gene Expression (Cage)","volume":"28 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2009-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"121808901","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Transcription Regulatory Networks Analysis Using CAGE","authors":"J. Tegnér, J. Björkegren, T. Ravasi, V. Bajic","doi":"10.1201/9780429065750-12","DOIUrl":"https://doi.org/10.1201/9780429065750-12","url":null,"abstract":"Mapping out cellular networks in general and transcriptional networks in particular has proved to be a bottle-neck hampering our understanding of biological processes. Integrative approaches fusing computational and experimental technologies for decoding transcriptional networks at a high level of resolution is therefore of uttermost importance. Yet, this is challenging since the control of gene expression in eukaryotes is a complex multi-level process influenced by several epigenetic factors and the fine interplay between regulatory proteins and the promoter structure governing the combinatorial regulation of gene expression. In this chapter we review how the CAGE data can be integrated with other measurements such as expression, physical interactions and computational prediction of regulatory motifs, which together can provide a genome-wide picture of eukaryotic transcriptional regulatory networks at a new level of resolution.","PeriodicalId":182337,"journal":{"name":"Cap-Analysis Gene Expression (Cage)","volume":"53 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2009-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"130555391","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Extraction and Quality Control of CAGE Tags","authors":"E. Arner, T. Lassmann","doi":"10.1201/9780429065750-7","DOIUrl":"https://doi.org/10.1201/9780429065750-7","url":null,"abstract":"","PeriodicalId":182337,"journal":{"name":"Cap-Analysis Gene Expression (Cage)","volume":"36 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2009-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"130112597","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Comparative Genomics and Mammalian Promoter Evolution","authors":"Martin S. Taylor, Gregory E. Jordan, C. Semple","doi":"10.1201/9780429065750-16","DOIUrl":"https://doi.org/10.1201/9780429065750-16","url":null,"abstract":"","PeriodicalId":182337,"journal":{"name":"Cap-Analysis Gene Expression (Cage)","volume":"25 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2009-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"115123856","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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