Literature DB >> 16443930

siRecords: an extensive database of mammalian siRNAs with efficacy ratings.

Yongliang Ren1, Wuming Gong, Qiqi Xu, Xin Zheng, Dong Lin, Yejun Wang, Tongbin Li.   

Abstract

UNLABELLED: Short interfering RNAs (siRNAs) have been gaining popularity as the gene knock-down tool of choice by many researchers because of the clean nature of their workings as well as the technical simplicity and cost efficiency in their applications. We have constructed siRecords, a database of siRNAs experimentally tested by researchers with consistent efficacy ratings. This database will help siRNA researchers develop more reliable siRNA design rules; in the mean time, siRecords will benefit experimental researchers directly by providing them with information about the siRNAs that have been experimentally tested against the genes of their interest. Currently, more than 4100 carefully annotated siRNA sequences obtained from more than 1200 published siRNA studies are hosted in siRecords. This database will continue to expand as more experimentally tested siRNAs are published. AVAILABILITY: The siRecords database can be accessed at http://siRecords.umn.edu/siRecords/

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Year:  2006        PMID: 16443930     DOI: 10.1093/bioinformatics/btl026

Source DB:  PubMed          Journal:  Bioinformatics        ISSN: 1367-4803            Impact factor:   6.937


  16 in total

Review 1.  Toward a complete in silico, multi-layered embryonic stem cell regulatory network.

Authors:  Huilei Xu; Christoph Schaniel; Ihor R Lemischka; Avi Ma'ayan
Journal:  Wiley Interdiscip Rev Syst Biol Med       Date:  2010 Nov-Dec

2.  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

3.  Multi-task learning for cross-platform siRNA efficacy prediction: an in-silico study.

Authors:  Qi Liu; Qian Xu; Vincent W Zheng; Hong Xue; Zhiwei Cao; Qiang Yang
Journal:  BMC Bioinformatics       Date:  2010-04-10       Impact factor: 3.169

4.  Secondary RNA structure and its role in RNA interference to silence the respiratory syncytial virus fusion protein gene.

Authors:  Komal Vig; Nuruddeen Lewis; Eddie G Moore; Shreekumar Pillai; Vida A Dennis; Shree R Singh
Journal:  Mol Biotechnol       Date:  2009-06-09       Impact factor: 2.695

5.  mRNA turnover rate limits siRNA and microRNA efficacy.

Authors:  Erik Larsson; Chris Sander; Debora Marks
Journal:  Mol Syst Biol       Date:  2010-11-16       Impact factor: 11.429

6.  VIRsiRNAdb: a curated database of experimentally validated viral siRNA/shRNA.

Authors:  Nishant Thakur; Abid Qureshi; Manoj Kumar
Journal:  Nucleic Acids Res       Date:  2011-12-01       Impact factor: 16.971

7.  Reconsideration of in-silico siRNA design based on feature selection: a cross-platform data integration perspective.

Authors:  Qi Liu; Han Zhou; Juan Cui; Zhiwei Cao; Ying Xu
Journal:  PLoS One       Date:  2012-05-24       Impact factor: 3.240

8.  An accurate and interpretable model for siRNA efficacy prediction.

Authors:  Jean-Philippe Vert; Nicolas Foveau; Christian Lajaunie; Yves Vandenbrouck
Journal:  BMC Bioinformatics       Date:  2006-11-30       Impact factor: 3.169

9.  Integrated siRNA design based on surveying of features associated with high RNAi effectiveness.

Authors:  Wuming Gong; Yongliang Ren; Qiqi Xu; Yejun Wang; Dong Lin; Haiyan Zhou; Tongbin Li
Journal:  BMC Bioinformatics       Date:  2006-11-27       Impact factor: 3.169

10.  sIR: siRNA Information Resource, a web-based tool for siRNA sequence design and analysis and an open access siRNA database.

Authors:  Jyoti K Shah; Harold R Garner; Michael A White; David S Shames; John D Minna
Journal:  BMC Bioinformatics       Date:  2007-05-31       Impact factor: 3.169

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