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siRNA DataBase with Thermodynamic & Composition Information
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The database includes siRNA screening experiments reported in the literature. Activity values is expressed
as the ratio of the level of a particular mRNA or protein measured in cells after treatment with the experimental
siRNA oligonucleotide duplex versus the level of the same mRNA or protein measured in untreated cells.
For correlation analysis natural logarithmic values of the activity values were used.
Thermodynamic properties for oligonucleotides and relevant duplexes were calculated using program OligoWalk from software
package RNAstructure 3.71, that is a Windows implementation
of the Zuker algorithm for RNA secondary structure prediction based on free energy minimization (Mathews, D.H.;
Sabina, J.; Zuker, M.; and Turner, D.H., "Expanded Sequence Dependence of Thermodynamic Parameters Improves
Prediction of RNA Secondary Structure", Journal of Molecular Biology, 1999, 288, 911-940).
Thermodynamic parameters for each base pair couple in the sense-antisense RNA oligonucleotide
duplex were calculated using Excel Macro "RNA-RNA positional report" created by DNA Software Inc.
Download of the database is available in a format of .xls file (Microsoft Excel).
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