Literature DB >> 15215364

siDirect: highly effective, target-specific siRNA design software for mammalian RNA interference.

Yuki Naito1, Tomoyuki Yamada, Kumiko Ui-Tei, Shinichi Morishita, Kaoru Saigo.   

Abstract

siDirect (http://design.RNAi.jp/) is a web-based online software system for computing highly effective small interfering RNA (siRNA) sequences with maximum target-specificity for mammalian RNA interference (RNAi). Highly effective siRNA sequences are selected using novel guidelines that were established through an extensive study of the relationship between siRNA sequences and RNAi activity. Our efficient software avoids off-target gene silencing to enumerate potential cross-hybridization candidates that the widely used BLAST search may overlook. The website accepts an arbitrary sequence as input and quickly returns siRNA candidates, providing a wide scope of applications in mammalian RNAi, including systematic functional genomics and therapeutic gene silencing.

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Year:  2004        PMID： 15215364      PMCID： PMC441580          DOI： 10.1093/nar/gkh442

Source DB:  PubMed          Journal:  Nucleic Acids Res        ISSN： 0305-1048            Impact factor:   16.971


  21 in total

1.  RNA interference is mediated by 21- and 22-nucleotide RNAs.

Authors:  S M Elbashir; W Lendeckel; T Tuschl
Journal:  Genes Dev       Date:  2001-01-15       Impact factor: 11.361

Review 2.  RNA interference.

Authors:  Gregory J Hannon
Journal:  Nature       Date:  2002-07-11       Impact factor: 49.962

Review 3.  Killing the messenger: short RNAs that silence gene expression.

Authors:  Derek M Dykxhoorn; Carl D Novina; Phillip A Sharp
Journal:  Nat Rev Mol Cell Biol       Date:  2003-06       Impact factor: 94.444

4.  Expression profiling reveals off-target gene regulation by RNAi.

Authors:  Aimee L Jackson; Steven R Bartz; Janell Schelter; Sumire V Kobayashi; Julja Burchard; Mao Mao; Bin Li; Guy Cavet; Peter S Linsley
Journal:  Nat Biotechnol       Date:  2003-05-18       Impact factor: 54.908

5.  Basic local alignment search tool.

Authors:  S F Altschul; W Gish; W Miller; E W Myers; D J Lipman
Journal:  J Mol Biol       Date:  1990-10-05       Impact factor: 5.469

6.  Single-stranded antisense siRNAs guide target RNA cleavage in RNAi.

Authors:  Javier Martinez; Agnieszka Patkaniowska; Henning Urlaub; Reinhard Lührmann; Thomas Tuschl
Journal:  Cell       Date:  2002-09-06       Impact factor: 41.582

7.  Stable suppression of tumorigenicity by virus-mediated RNA interference.

Authors:  Thijn R Brummelkamp; René Bernards; Reuven Agami
Journal:  Cancer Cell       Date:  2002-09       Impact factor: 31.743

Review 8.  Mammalian RNAi for the masses.

Authors:  Yang Shi
Journal:  Trends Genet       Date:  2003-01       Impact factor: 11.639

9.  Database resources of the National Center for Biotechnology.

Authors:  David L Wheeler; Deanna M Church; Scott Federhen; Alex E Lash; Thomas L Madden; Joan U Pontius; Gregory D Schuler; Lynn M Schriml; Edwin Sequeira; Tatiana A Tatusova; Lukas Wagner
Journal:  Nucleic Acids Res       Date:  2003-01-01       Impact factor: 16.971

10.  Short-interfering-RNA-mediated gene silencing in mammalian cells requires Dicer and eIF2C translation initiation factors.

Authors:  Noboru Doi; Shuhei Zenno; Ryu Ueda; Hiroko Ohki-Hamazaki; Kumiko Ui-Tei; Kaoru Saigo
Journal:  Curr Biol       Date:  2003-01-08       Impact factor: 10.834
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  76 in total

1.  Efficient prediction of siRNAs with siRNArules 1.0: an open-source JAVA approach to siRNA algorithms.

Authors:  Torgeir Holen
Journal:  RNA       Date:  2006-07-26       Impact factor: 4.942

2.  Optimization and functional effects of stable short hairpin RNA expression in primary human lymphocytes via lentiviral vectors.

Authors:  Dong Sung An; F Xiao-Feng Qin; Vincent C Auyeung; Si Hua Mao; Sam K P Kung; David Baltimore; Irvin S Y Chen
Journal:  Mol Ther       Date:  2006-07-17       Impact factor: 11.454

3.  TTLL7 is a mammalian beta-tubulin polyglutamylase required for growth of MAP2-positive neurites.

Authors:  Koji Ikegami; Masahiro Mukai; Jun-ichi Tsuchida; Robb L Heier; Grant R Macgregor; Mitsutoshi Setou
Journal:  J Biol Chem       Date:  2006-08-09       Impact factor: 5.157

Review 4.  RNAi in embryonic stem cells.

Authors:  Li Ding; Frank Buchholz
Journal:  Stem Cell Rev       Date:  2006       Impact factor: 5.739

5.  Increased potency and longevity of gene silencing using validated Dicer substrates.

Authors:  E Hefner; K Clark; C Whitman; M A Behlke; S D Rose; A S Peek; T Rubio
Journal:  J Biomol Tech       Date:  2008-09

6.  Ubiquitin carboxyl-terminal esterase L1 promotes proliferation of human choroidal and retinal endothelial cells.

Authors:  Yuzhen Pan; Binoy Appukuttan; Kathleen Mohs; Liam M Ashander; Justine R Smith
Journal:  Asia Pac J Ophthalmol (Phila)       Date:  2015 Jan-Feb

7.  RiboSubstrates: a web application addressing the cleavage specificities of ribozymes in designated genomes.

Authors:  Jean-François Lucier; Lucien Junior Bergeron; Francis P Brière; Rodney Ouellette; Sherif Abou Elela; Jean-Pierre Perreault
Journal:  BMC Bioinformatics       Date:  2006-10-31       Impact factor: 3.169

8.  Pituitary tumor-transforming 1 increases cell motility and promotes lymph node metastasis in esophageal squamous cell carcinoma.

Authors:  Tetsuo Ito; Yutaka Shimada; Takatsugu Kan; Stefan David; Yulan Cheng; Yuriko Mori; Rachana Agarwal; Bogdan Paun; Zhe Jin; Alexandru Olaru; James P Hamilton; Jian Yang; John M Abraham; Stephen J Meltzer; Fumiaki Sato
Journal:  Cancer Res       Date:  2008-05-01       Impact factor: 12.701

9.  Therapeutic potential of RNA interference in pain medicine.

Authors:  Ping-Heng Tan; Lin-Cheng Yang; Ru-Rong Ji
Journal:  Open Pain J       Date:  2009-01-01

10.  RNAi induced in mammalian and Drosophila cells via transfection of dimers and trimers of small interfering RNA.

Authors:  Kumiko Ui-Tei; Shuhei Zenno; Aya Juni; Kaoru Saigo
Journal:  J RNAi Gene Silencing       Date:  2005-10-14
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