DREAM: a webserver for the identification of editing sites in mature miRNAs using deep sequencing data

被引：16

作者：

Alon, Shahar ^{[1
,2
]}

Erew, Muhammad ^{[3
]}

Eisenberg, Eli ^{[2
,3
]}

机构：

[1] Tel Aviv Univ, George S Wise Fac Life Sci, Dept Neurobiol, IL-69978 Tel Aviv, Israel

[2] Tel Aviv Univ, Sagol Sch Neurosci, IL-69978 Tel Aviv, Israel

[3] Tel Aviv Univ, Raymond & Beverly Sackler Sch Phys & Astron, IL-69978 Tel Aviv, Israel

来源：

BIOINFORMATICS | 2015年 / 31卷 / 15期

基金：

以色列科学基金会;

关键词：

HUMAN TRANSCRIPTOME; ADAR DEAMINASES; WIDESPREAD RNA; MICRORNAS; EXPRESSION; BRAIN;

D O I：

10.1093/bioinformatics/btv187

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

DREAM: detecting RNA editing associated with microRNAs, is a webserver for the identification of mature microRNA editing events using deep sequencing data. Raw microRNA sequencing reads can be provided as input, the reads are aligned against the genome and custom scripts process the data, search for potential editing sites and assess the statistical significance of the findings. The output is a text file with the location and the statistical description of all the putative editing sites detected.

引用

页码：2568 / 2570

页数：3

共 18 条

[1]

Alon S, 2015, METHODS MOL BIOL, V1269, P231, DOI 10.1007/978-1-4939-2291-8_14

[2]

Alon S, 2013, METHODS MOL BIOL, V1038, P159, DOI 10.1007/978-1-62703-514-9_9

[3] Systematic identification of edited microRNAs in the human brain [J].

Alon, Shahar ;

Mor, Eyal ;

Vigneault, Francois ;

Church, George M. ;

Locatelli, Franco ;

Galeano, Federica ;

Gallo, Angela ;

Shomron, Noam ;

Eisenberg, Eli .

GENOME RESEARCH, 2012, 22 (08) :1533-1540

[4] MicroRNAs: Genomics, biogenesis, mechanism, and function (Reprinted from Cell, vol 116, pg 281-297, 2004) [J].

Bartel, David P. .

CELL, 2007, 131 (04) :11-29

[5] Deep annotation of Drosophila melanogaster microRNAs yields insights into their processing, modification, and emergence [J].

Berezikov, Eugene ;

Robine, Nicolas ;

Samsonova, Anastasia ;

Westholm, Jakub O. ;

Naqvi, Ammar ;

Hung, Jui-Hung ;

Okamura, Katsutomo ;

Dai, Qi ;

Bortolamiol-Becet, Diane ;

Martin, Raquel ;

Zhao, Yongjun ;

Zamore, Phillip D. ;

Hannon, Gregory J. ;

Marra, Marco A. ;

Weng, Zhiping ;

Perrimon, Norbert ;

Lai, Eric C. .

GENOME RESEARCH, 2011, 21 (02) :203-215

[6] A comprehensive survey of 3′ animal miRNA modification events and a possible role for 3′ adenylation in modulating miRNA targeting effectiveness [J].

Burroughs, A. Maxwell ;

Ando, Yoshinari ;

de Hoon, Michiel J. L. ;

Tomaru, Yasuhiro ;

Nishibu, Takahiro ;

Ukekawa, Ryo ;

Funakoshi, Taku ;

Kurokawa, Tsutomu ;

Suzuki, Harukazu ;

Hayashizaki, Yoshihide ;

Daub, Carsten O. .

GENOME RESEARCH, 2010, 20 (10) :1398-1410

[7] ADAR mediates differential expression of polycistronic microRNAs [J].

Chawla, Geetanjali ;

Sokol, Nicholas S. .

NUCLEIC ACIDS RESEARCH, 2014, 42 (08) :5245-5255

[8] Cross-mapping and the identification of editing sites in mature microRNAs in high-throughput sequencing libraries [J].

de Hoon, Michiel J. L. ;

Taft, Ryan J. ;

Hashimoto, Takehiro ;

Kanamori-Katayama, Mutsumi ;

Kawaji, Hideya ;

Kawano, Mitsuoki ;

Kishima, Mami ;

Lassmann, Timo ;

Faulkner, Geoffrey J. ;

Mattick, John S. ;

Daub, Carsten O. ;

Carninci, Piero ;

Kawai, Jun ;

Suzuki, Harukazu ;

Hayashizaki, Yoshihide .

GENOME RESEARCH, 2010, 20 (02) :257-264

[9] A-to-I editing of microRNAs in the mammalian brain increases during development [J].

Ekdahl, Ylva ;

Farahani, Hossein Shahrabi ;

Behm, Mikaela ;

Lagergren, Jens ;

Ohman, Marie .

GENOME RESEARCH, 2012, 22 (08) :1477-1487

[10] Redirection of silencing targets by adenosine-to-inosine editing of miRNAs [J].

Kawahara, Yukio ;

Zinshteyn, Boris ;

Sethupathy, Praveen ;

Iizasa, Hisashi ;

Hatzigeorgiou, Artemis G. ;

Nishikura, Kazuko .

SCIENCE, 2007, 315 (5815) :1137-1140

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