RPFdb: a database for genome wide information of translated mRNA generated from ribosome profiling
dc.citation.doi | 10.1093/nar/gkv972 | |
dc.citation.epage | D258 | |
dc.citation.issn | 0305-1048 | |
dc.citation.issue | D1 | |
dc.citation.jtitle | Nucleic Acids Research | |
dc.citation.spage | D254 | |
dc.citation.volume | 44 | |
dc.contributor.author | Xie, S. Q. | |
dc.contributor.author | Nie, P. | |
dc.contributor.author | Wang, Y. | |
dc.contributor.author | Wang, H. W. | |
dc.contributor.author | Li, H. Y. | |
dc.contributor.author | Yang, Zhilong L. | |
dc.contributor.author | Liu, Y. Z. | |
dc.contributor.author | Ren, J. | |
dc.contributor.author | Xie, Z. | |
dc.contributor.authoreid | zyang | |
dc.date.accessioned | 2016-09-20T14:53:42Z | |
dc.date.available | 2016-09-20T14:53:42Z | |
dc.date.published | 2016 | |
dc.description | Citation: Xie, S. Q., Nie, P., Wang, Y., Wang, H. W., Li, H. Y., Yang, Z. L., . . . Xie, Z. (2016). RPFdb: a database for genome wide information of translated mRNA generated from ribosome profiling. Nucleic Acids Research, 44(D1), D254-D258. doi:10.1093/nar/gkv972 | |
dc.description.abstract | Translational control is crucial in the regulation of gene expression and deregulation of translation is associated with a wide range of cancers and human diseases. Ribosome profiling is a technique that provides genome wide information of mRNA in translation based on deep sequencing of ribosome protected mRNA fragments (RPF). RPFdb is a comprehensive resource for hosting, analyzing and visualizing RPF data, available at www.rpfdb.org or http://sysbio.sysu.edu.cn/rpfdb/index. html. The current version of database contains 777 samples from 82 studies in 8 species, processed and reanalyzed by a unified pipeline. There are two ways to query the database: by keywords of studies or by genes. The outputs are presented in three levels. (i) Study level: including meta information of studies and reprocessed data for gene expression of translated mRNAs; (ii) Sample level: including global perspective of translated mRNA and a list of the most translated mRNA of each sample from a study; (iii) Gene level: including normalized sequence counts of translated mRNA on different genomic location of a gene from multiple samples and studies. To explore rich information provided by RPF, RPFdb also provides a genome browser to query and visualize context-specific translated mRNA. Overall our database provides a simple way to search, analyze, compare, visualize and download RPF data sets. | |
dc.identifier.uri | http://hdl.handle.net/2097/33950 | |
dc.relation.uri | https://doi.org/10.1093/nar/gkv972 | |
dc.rights | Attribution 4.0 International (CC BY 4.0) | |
dc.rights.uri | https://creativecommons.org/licenses/by/4.0/ | |
dc.subject | In-Vivo | |
dc.subject | Seq | |
dc.subject | Reveals | |
dc.subject | Cells | |
dc.subject | Biochemistry & Molecular Biology | |
dc.title | RPFdb: a database for genome wide information of translated mRNA generated from ribosome profiling | |
dc.type | Article |
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