circBase: a database for circular RNAs

被引：1732

作者：

Glazar, Petar ^{[1
]}

Papavasileiou, Panagiotis ^{[1
]}

Rajewsky, Nikolaus ^{[1
]}

机构：

[1] Max Delbruck Ctr Mol Med, D-13125 Berlin, Germany

来源：

RNA | 2014年 / 20卷 / 11期

关键词：

gene expression; circular RNA; database; GENOME BROWSER;

D O I：

10.1261/rna.043687.113

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

070307 [化学生物学]; 071010 [生物化学与分子生物学];

摘要：

Recently, several laboratories have reported thousands of circular RNAs (circRNAs) in animals. Numerous circRNAs are highly stable and have specific spatiotemporal expression patterns. Even though a function for circRNAs is unknown, these features make circRNAs an interesting class of RNAs as possible biomarkers and for further research. We developed a database and website, "circBase," where merged and unified data sets of circRNAs and the evidence supporting their expression can be accessed, downloaded, and browsed within the genomic context. circBase also provides scripts to identify known and novel circRNAs in sequencing data.

引用

页码：1666 / 1670

页数：5

共 22 条

[1]

The African coelacanth genome provides insights into tetrapod evolution [J].

Amemiya, Chris T. ;

Alfoeldi, Jessica ;

Lee, Alison P. ;

Fan, Shaohua ;

Philippe, Herve ;

MacCallum, Iain ;

Braasch, Ingo ;

Manousaki, Tereza ;

Schneider, Igor ;

Rohner, Nicolas ;

Organ, Chris ;

Chalopin, Domitille ;

Smith, Jeramiah J. ;

Robinson, Mark ;

Dorrington, Rosemary A. ;

Gerdol, Marco ;

Aken, Bronwen ;

Biscotti, Maria Assunta ;

Barucca, Marco ;

Baurain, Denis ;

Berlin, Aaron M. ;

Blatch, Gregory L. ;

Buonocore, Francesco ;

Burmester, Thorsten ;

Campbell, Michael S. ;

Canapa, Adriana ;

Cannon, John P. ;

Christoffels, Alan ;

De Moro, Gianluca ;

Edkins, Adrienne L. ;

Fan, Lin ;

Fausto, Anna Maria ;

Feiner, Nathalie ;

Forconi, Mariko ;

Gamieldien, Junaid ;

Gnerre, Sante ;

Gnirke, Andreas ;

Goldstone, Jared V. ;

Haerty, Wilfried ;

Hahn, Mark E. ;

Hesse, Uljana ;

Hoffmann, Steve ;

Johnson, Jeremy ;

Karchner, Sibel I. ;

Kuraku, Shigehiro ;

Lara, Marcia ;

Levin, Joshua Z. ;

Litman, Gary W. ;

Mauceli, Evan ;

Miyake, Tsutomu .

NATURE, 2013, 496 (7445) :311-316

[2]

doRiNA: a database of RNA interactions in post-transcriptional regulation [J].

Anders, Gerd ;

Mackowiak, Sebastian D. ;

Jens, Marvin ;

Maaskola, Jonas ;

Kuntzagk, Andreas ;

Rajewsky, Nikolaus ;

Landthaler, Markus ;

Dieterich, Christoph .

NUCLEIC ACIDS RESEARCH, 2012, 40 (D1) :D180-D186

[3]

WormBase:: a comprehensive data resource for Caenorhabditis biology and genomics [J].

Chen, NS ;

Harris, TW ;

Antoshechkin, I ;

Bastiani, C ;

Bieri, T ;

Blasiar, D ;

Bradnam, K ;

Canaran, P ;

Chan, J ;

Chen, CK ;

Chen, WJ ;

Cunningham, F ;

Davis, P ;

Kenny, E ;

Kishore, R ;

Lawson, D ;

Lee, R ;

Muller, HM ;

Nakamura, C ;

Pai, S ;

Ozersky, P ;

Petcherski, A ;

Rogers, A ;

Sab, A ;

Schwarz, EM ;

Van Auken, K ;

Wang, QH ;

Durbin, R ;

Spieth, J ;

Sternberg, PW ;

Stein, LD .

NUCLEIC ACIDS RESEARCH, 2005, 33 :D383-D389

[4]

The Comprehensive Phytopathogen Genomics Resource: a web-based resource for data-mining plant pathogen genomes [J].

Hamilton, John P. ;

Neeno-Eckwall, Eric C. ;

Adhikari, Bishwo N. ;

Perna, Nicole T. ;

Tisserat, Ned ;

Leach, Jan E. ;

Levesque, C. Andre ;

Buell, C. Robin .

DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION, 2011,

[5]

Natural RNA circles function as efficient microRNA sponges [J].

Hansen, Thomas B. ;

Jensen, Trine I. ;

Clausen, Bettina H. ;

Bramsen, Jesper B. ;

Finsen, Bente ;

Damgaard, Christian K. ;

Kjems, Jorgen .

NATURE, 2013, 495 (7441) :384-388

[6]

A multi-split mapping algorithm for circular RNA, splicing, trans-splicing and fusion detection [J].

Hoffmann, Steve ;

Otto, Christian ;

Doose, Gero ;

Tanzer, Andrea ;

Langenberger, David ;

Christ, Sabina ;

Kunz, Manfred ;

Holdt, Lesca M. ;

Teupser, Daniel ;

Hackermueller, Joerg ;

Stadler, Peter F. .

GENOME BIOLOGY, 2014, 15 (02)

[7]

An RNA-Seq Strategy to Detect the Complete Coding and Non-Coding Transcriptome Including Full-Length Imprinted Macro ncRNAs [J].

Huang, Ru ;

Jaritz, Markus ;

Guenzl, Philipp ;

Vlatkovic, Irena ;

Sommer, Andreas ;

Tamir, Ido M. ;

Marks, Hendrik ;

Klampfl, Thorsten ;

Kralovics, Robert ;

Stunnenberg, Hendrik G. ;

Barlow, Denise P. ;

Pauler, Florian M. .

PLOS ONE, 2011, 6 (11)

[8]

Detecting and characterizing circular RNAs [J].

Jeck, William R. ;

Sharpless, Norman E. .

NATURE BIOTECHNOLOGY, 2014, 32 (05) :453-461

[9]

Circular RNAs are abundant, conserved, and associated with ALU repeats [J].

Jeck, William R. ;

Sorrentino, Jessica A. ;

Wang, Kai ;

Slevin, Michael K. ;

Burd, Christin E. ;

Liu, Jinze ;

Marzluff, William F. ;

Sharpless, Norman E. .

RNA, 2013, 19 (02) :141-157

[10]

The human genome browser at UCSC [J].

Kent, WJ ;

Sugnet, CW ;

Furey, TS ;

Roskin, KM ;

Pringle, TH ;

Zahler, AM ;

Haussler, D .

GENOME RESEARCH, 2002, 12 (06) :996-1006

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