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siRNAdb: a database of siRNA sequences
Alistair M Chalk1, Richard E Warfinge, Patrick Georgii-Hemming
1Center for Genomics and Bioinformatics, Karolinska Institutet, Berzelius väg 35, S-171 77 Stockholm, Sweden. alistair.chalk@cgb.ki.se
Nucleic Acids Research
|December 21, 2004
Summary
The siRNA database offers a gene-centric view of experimental data for short interfering RNAs (siRNAs) used in gene knockdown. It helps researchers evaluate siRNA efficacy and potential off-target effects before experiments.
Area of Science:
- Molecular Biology
- Bioinformatics
- Genetics
Background:
- Short interfering RNAs (siRNAs) are widely used for gene knockdown by degrading target messenger RNA (mRNA).
- Evaluating existing siRNA knockdown experiments is crucial for experimental planning and success.
- A centralized resource for siRNA efficacy and safety data is needed.
Purpose of the Study:
- To present the siRNA database, a gene-centric resource for siRNA experimental data.
- To provide information on siRNAs with known and predicted high efficacy.
- To enable users to assess siRNA inhibition potential and off-target effects.
Main Methods:
- The database aggregates and presents siRNA sequences and their experimental efficacy.
- It includes predictions of high-efficacy siRNAs using multiple methods.
- Information on siRNA thermodynamic properties and potential off-target effects is linked to sequences.
Main Results:
- The siRNA database offers a comprehensive, gene-centric view of siRNA experimental data.
- It includes siRNAs with validated efficacy and those predicted to be highly effective.
- Data on thermodynamic properties and off-target effects are integrated for user evaluation.
Conclusions:
- The siRNA database serves as a valuable tool for researchers planning gene knockdown experiments.
- It facilitates the evaluation of siRNA efficacy and potential sequence-specific off-target effects.
- The database promotes informed selection of siRNAs, improving experimental outcomes.