siRNAdb

siRNAdb provides a gene-centric database of experimentally validated and predicted small interfering RNAs (siRNAs), including thermodynamic properties and off-target search via siSearch and AOSearch to support design and evaluation of siRNA-mediated mRNA knockdown.

Key Features:

• Gene-Centric Database: A gene-centered compilation of siRNA experimental data linking siRNAs to specific target genes and prior knockdown experiments.
• Efficacy Evaluation: Contains both known efficacious siRNAs and siRNAs predicted to be highly effective using a combination of analytical methods.
• Thermodynamic Properties: Associates detailed thermodynamic property data with each siRNA sequence to inform stability and functionality predictions.
• Off-Target Effects Analysis: Provides sequence-specific assessments of potential off-target effects to identify unintended interactions.
• Non-Specific Match Search (AOSearch): Integrates AOSearch to identify non-specific matches and potential cross-reactivity with other genomic sequences.
• siSearch Integration: Includes siSearch for mining siRNA data and querying experimental records related to siRNA performance.

Scientific Applications:

• siRNA design and selection: Supports selection of siRNAs for mRNA knockdown experiments by providing efficacy, thermodynamic, and specificity data.
• Gene function analysis: Facilitates functional genomics studies by linking siRNA reagents to experimental knockdown outcomes.
• Therapeutic development: Aids preclinical evaluation of siRNA candidates by assessing predicted efficacy and off-target risk.
• Off-target mitigation: Enables identification and reduction of potential sequence-specific off-target effects and cross-reactivity in experimental planning.

Methodology:

siRNAdb compiles experimental siRNA data, records known efficacious and predicted siRNA performance from multiple analytical methods, links thermodynamic property analyses to each sequence, and assesses potential off-target and non-specific matches using siSearch and AOSearch.