DIANA-microT web server v5.0: service integration into miRNA functional analysis workflows

被引：908

作者：

Paraskevopoulou, Maria D. ^{[1
,2
]}

Georgakilas, Georgios ^{[1
,2
]}

Kostoulas, Nikos ^{[3
]}

Vlachos, Ioannis S. ^{[1
,4
]}

Vergoulis, Thanasis ^{[3
]}

Reczko, Martin ^{[1
]}

Filippidis, Christos ^{[5
]}

Dalamagas, Theodore ^{[3
]}

Hatzigeorgiou, A. G. ^{[1
,2
]}

机构：

[1] Biomed Sci Res Ctr Alexander Fleming, DIANA Lab, Vari 16672, Greece

[2] Univ Thessaly, Dept Comp & Commun Engn, Volos 38221, Greece

[3] Athena Res Ctr, IMIS Inst, Athens 11524, Greece

[4] Univ Athens, Med Sch Athens, Lab Expt Surg & Surg Res NS Christeas, Athens 11527, Greece

[5] Natl Ctr Sci Res Demokritos, Inst Nucl & Particle Phys, Aghia Paraskevi 15310, Greece

来源：

NUCLEIC ACIDS RESEARCH | 2013年 / 41卷 / W1期

关键词：

TARGETS;

D O I：

10.1093/nar/gkt393

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

MicroRNAs (miRNAs) are small endogenous RNA molecules that regulate gene expression through mRNA degradation and/or translation repression, affecting many biological processes. DIANA-microT web server (http://www.microrna.gr/webServer) is dedicated to miRNA target prediction/functional analysis, and it is being widely used from the scientific community, since its initial launch in 2009. DIANA-microT v5.0, the new version of the microT server, has been significantly enhanced with an improved target prediction algorithm, DIANA-microT-CDS. It has been updated to incorporate miRBase version 18 and Ensembl version 69. The in silico-predicted miRNA-gene interactions in Homo sapiens, Mus musculus, Drosophila melanogaster and Caenorhabditis elegans exceed 11 million in total. The web server was completely redesigned, to host a series of sophisticated workflows, which can be used directly from the on-line web interface, enabling users without the necessary bioinformatics infrastructure to perform advanced multi-step functional miRNA analyses. For instance, one available pipeline performs miRNA target prediction using different thresholds and meta-analysis statistics, followed by pathway enrichment analysis. DIANA-microT web server v5.0 also supports a complete integration with the Taverna Workflow Management System (WMS), using the in-house developed DIANA-Taverna Plug-in. This plug-in provides ready-to-use modules for miRNA target prediction and functional analysis, which can be used to form advanced high-throughput analysis pipelines.

引用

页码：W169 / W173

页数：5

共 16 条

[1] Lost in translation: an assessment and perspective for computational microRNA target identification [J].

Alexiou, Panagiotis ;

Maragkakis, Manolis ;

Papadopoulos, Giorgos L. ;

Reczko, Martin ;

Hatzigeorgiou, Artemis G. .

BIOINFORMATICS, 2009, 25 (23) :3049-3055

[2] MicroRNAs: Target Recognition and Regulatory Functions [J].

Bartel, David P. .

CELL, 2009, 136 (02) :215-233

[3] Ensembl 2012 [J].

Flicek, Paul ;

Amode, M. Ridwan ;

Barrell, Daniel ;

Beal, Kathryn ;

Brent, Simon ;

Carvalho-Silva, Denise ;

Clapham, Peter ;

Coates, Guy ;

Fairley, Susan ;

Fitzgerald, Stephen ;

Gil, Laurent ;

Gordon, Leo ;

Hendrix, Maurice ;

Hourlier, Thibaut ;

Johnson, Nathan ;

Kaehaeri, Andreas K. ;

Keefe, Damian ;

Keenan, Stephen ;

Kinsella, Rhoda ;

Komorowska, Monika ;

Koscielny, Gautier ;

Kulesha, Eugene ;

Larsson, Pontus ;

Longden, Ian ;

McLaren, William ;

Muffato, Matthieu ;

Overduin, Bert ;

Pignatelli, Miguel ;

Pritchard, Bethan ;

Riat, Harpreet Singh ;

Ritchie, Graham R. S. ;

Ruffier, Magali ;

Schuster, Michael ;

Sobral, Daniel ;

Tang, Y. Amy ;

Taylor, Kieron ;

Trevanion, Stephen ;

Vandrovcova, Jana ;

White, Simon ;

Wilson, Mark ;

Wilder, Steven P. ;

Aken, Bronwen L. ;

Birney, Ewan ;

Cunningham, Fiona ;

Dunham, Ian ;

Durbin, Richard ;

Fernandez-Suarez, Xose M. ;

Harrow, Jennifer ;

Herrero, Javier ;

Hubbard, Tim J. P. .

NUCLEIC ACIDS RESEARCH, 2012, 40 (D1) :D84-D90

[4] Taverna: a tool for building and running workflows of services [J].

Hull, Duncan ;

Wolstencroft, Katy ;

Stevens, Robert ;

Goble, Carole ;

Pocock, Mathew R. ;

Li, Peter ;

Oinn, Tom .

NUCLEIC ACIDS RESEARCH, 2006, 34 :W729-W732

[5] KEGG for integration and interpretation of large-scale molecular data sets [J].

Kanehisa, Minoru ;

Goto, Susumu ;

Sato, Yoko ;

Furumichi, Miho ;

Tanabe, Mao .

NUCLEIC ACIDS RESEARCH, 2012, 40 (D1) :D109-D114

[6] miRBase: integrating microRNA annotation and deep-sequencing data [J].

Kozomara, Ana ;

Griffiths-Jones, Sam .

NUCLEIC ACIDS RESEARCH, 2011, 39 :D152-D157

[7] A mammalian microRNA expression atlas based on small RNA library sequencing [J].

Landgraf, Pablo ;

Rusu, Mirabela ;

Sheridan, Robert ;

Sewer, Alain ;

Iovino, Nicola ;

Aravin, Alexei ;

Pfeffer, Sebastien ;

Rice, Amanda ;

Kamphorst, Alice O. ;

Landthaler, Markus ;

Lin, Carolina ;

Socci, Nicholas D. ;

Hermida, Leandro ;

Fulci, Valerio ;

Chiaretti, Sabina ;

Foa, Robin ;

Schliwka, Julia ;

Fuchs, Uta ;

Novosel, Astrid ;

Mueller, Roman-Ulrich ;

Schermer, Bernhard ;

Bissels, Ute ;

Inman, Jason ;

Phan, Quang ;

Chien, Minchen ;

Weir, David B. ;

Choksi, Ruchi ;

De Vita, Gabriella ;

Frezzetti, Daniela ;

Trompeter, Hans-Ingo ;

Hornung, Veit ;

Teng, Grace ;

Hartmann, Gunther ;

Palkovits, Miklos ;

Di Lauro, Robert ;

Wernet, Peter ;

Macino, Giuseppe ;

Rogler, Charles E. ;

Nagle, James W. ;

Ju, Jingyue ;

Papavasiliou, F. Nina ;

Benzing, Thomas ;

Lichter, Peter ;

Tam, Wayne ;

Brownstein, Michael J. ;

Bosio, Andreas ;

Borkhardt, Arndt ;

Russo, James J. ;

Sander, Chris ;

Zavolan, Mihaela .

CELL, 2007, 129 (07) :1401-1414

[8] THE C-ELEGANS HETEROCHRONIC GENE LIN-4 ENCODES SMALL RNAS WITH ANTISENSE COMPLEMENTARITY TO LIN-14 [J].

LEE, RC ;

FEINBAUM, RL ;

AMBROS, V .

CELL, 1993, 75 (05) :843-854

[9] ASYMPTOTIC OPTIMALITY OF FISHERS METHOD OF COMBINING INDEPENDENT TESTS [J].

LITTELL, RC ;

FOLKS, JL .

JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION, 1971, 66 (336) :802-805

[10] DIANA-microT Web server upgrade supports Fly and Worm miRNA target prediction and bibliographic miRNA to disease association [J].

Maragkakis, Manolis ;

Vergoulis, Thanasis ;

Alexiou, Panagiotis ;

Reczko, Martin ;

Plomaritou, Kyriaki ;

Gousis, Mixail ;

Kourtis, Kornilios ;

Koziris, Nectarios ;

Dalamagas, Theodore ;

Hatzigeorgiou, Artemis G. .

NUCLEIC ACIDS RESEARCH, 2011, 39 :W145-W148

← 1 2 →