SiRNAEfficacyDB: An Experimentally Supported Small Interfering RNA Efficacy Database

Overview

Journal IET Syst Biol

Publisher Wiley

Specialty Biology

Date 2024 Nov 14

PMID 39541343

Authors

Yang Zhang

Ting Yang

Yu Yang

Dongsheng Xu

Yucheng Hu

Shuo Zhang

Nanchao Luo

Lin Ning

Liping Ren

Affiliations

Soon will be listed here.

Abstract

Small interfering RNA (siRNA) has revolutionised biomedical research and drug development through precise post-transcriptional gene silencing technology. Despite its immense potential, siRNA therapy still faces technical challenges, such as delivery efficiency, targeting specificity, and molecular stability. To address these challenges and facilitate siRNA drug development, we have developed siRNAEfficacyDB, a comprehensive database that integrates experimentally validated siRNA efficacy data. This database contains 3544 siRNA records, covering 42 target genes and 5 cell lines. It provides detailed information on siRNA sequences, target genes, inhibition efficiencies, experimental techniques, cell lines, siRNA concentrations, and incubation times. siRNAEfficacyDB offers a user-friendly web interface that makes it easy to query, browse and analyse data, enabling efficient access to siRNA-related information. In summary, siRNAEfficacyDB provides a useful data foundation for siRNA drug design and optimisation, serving as a valuable resource for advancing computer-aided siRNA design research and nucleic acid drug development. siRNAEfficacyDB is freely available at https://cellknowledge.com.cn/siRNAEfficacy for non-commercial use.

Citing Articles

siRNAEfficacyDB: An experimentally supported small interfering RNA efficacy database.

Zhang Y, Yang T, Yang Y, Xu D, Hu Y, Zhang S IET Syst Biol. 2024; 18(6):199-207.

PMID: 39541343 PMC: 11665841. DOI: 10.1049/syb2.12102.

References

Zhang Y, Pan X, Shi T, Gu Z, Yang Z, Liu M . P450Rdb: A manually curated database of reactions catalyzed by cytochrome P450 enzymes. J Adv Res. 2023; 63:35-42. PMC: 11380020. DOI: 10.1016/j.jare.2023.10.012. View

Lu Z, Mathews D . Efficient siRNA selection using hybridization thermodynamics. Nucleic Acids Res. 2007; 36(2):640-7. PMC: 2241856. DOI: 10.1093/nar/gkm920. View

Bai Y, Zhong H, Wang T, Lu Z . OligoFormer: an accurate and robust prediction method for siRNA design. Bioinformatics. 2024; 40(10). PMC: 11494384. DOI: 10.1093/bioinformatics/btae577. View

Amarzguioui M, Prydz H . An algorithm for selection of functional siRNA sequences. Biochem Biophys Res Commun. 2004; 316(4):1050-8. DOI: 10.1016/j.bbrc.2004.02.157. View

Huesken D, Lange J, Mickanin C, Weiler J, Asselbergs F, Warner J . Design of a genome-wide siRNA library using an artificial neural network. Nat Biotechnol. 2005; 23(8):995-1001. DOI: 10.1038/nbt1118. View

Ichihara M, Murakumo Y, Masuda A, Matsuura T, Asai N, Jijiwa M . Thermodynamic instability of siRNA duplex is a prerequisite for dependable prediction of siRNA activities. Nucleic Acids Res. 2007; 35(18):e123. PMC: 2094068. DOI: 10.1093/nar/gkm699. View

Ui-Tei K, Naito Y, Takahashi F, Haraguchi T, Ohki-Hamazaki H, Juni A . Guidelines for the selection of highly effective siRNA sequences for mammalian and chick RNA interference. Nucleic Acids Res. 2004; 32(3):936-48. PMC: 373388. DOI: 10.1093/nar/gkh247. View

Dong Y, Siegwart D, Anderson D . Strategies, design, and chemistry in siRNA delivery systems. Adv Drug Deliv Rev. 2019; 144:133-147. PMC: 6745264. DOI: 10.1016/j.addr.2019.05.004. View

Pan X, Ren L, Yang Y, Xu Y, Ning L, Zhang Y . MCSdb, a database of proteins residing in membrane contact sites. Sci Data. 2024; 11(1):281. PMC: 10923927. DOI: 10.1038/s41597-024-03104-7. View

10.

Ren Y, Gong W, Zhou H, Wang Y, Xiao F, Li T . siRecords: a database of mammalian RNAi experiments and efficacies. Nucleic Acids Res. 2008; 37(Database issue):D146-9. PMC: 2686443. DOI: 10.1093/nar/gkn817. View

11.

Zhang Y, Liu C, Liu M, Liu T, Lin H, Huang C . Attention is all you need: utilizing attention in AI-enabled drug discovery. Brief Bioinform. 2024; 25(1). PMC: 10772984. DOI: 10.1093/bib/bbad467. View

12.

Khvorova A . siRNAs-A New Class of Medicines. JAMA. 2023; 329(24):2185-2186. DOI: 10.1001/jama.2023.4570. View

13.

Takasaki S, Kotani S, Konagaya A . An effective method for selecting siRNA target sequences in mammalian cells. Cell Cycle. 2004; 3(6):790-5. View

14.

Han Y, He F, Chen Y, Liu Y, Yu H . SiRNA silencing efficacy prediction based on a deep architecture. BMC Genomics. 2018; 19(Suppl 7):669. PMC: 6157246. DOI: 10.1186/s12864-018-5028-8. View

15.

Hu X, Hipolito S, Lynn R, Abraham V, Ramos S, Wong-Staal F . Relative gene-silencing efficiencies of small interfering RNAs targeting sense and antisense transcripts from the same genetic locus. Nucleic Acids Res. 2004; 32(15):4609-17. PMC: 516062. DOI: 10.1093/nar/gkh790. View

16.

Jadhav V, Vaishnaw A, FitzGerald K, Maier M . RNA interference in the era of nucleic acid therapeutics. Nat Biotechnol. 2024; 42(3):394-405. DOI: 10.1038/s41587-023-02105-y. View

17.

Reynolds A, Leake D, Boese Q, Scaringe S, Marshall W, Khvorova A . Rational siRNA design for RNA interference. Nat Biotechnol. 2004; 22(3):326-30. DOI: 10.1038/nbt936. View

18.

Katoh T, Suzuki T . Specific residues at every third position of siRNA shape its efficient RNAi activity. Nucleic Acids Res. 2007; 35(4):e27. PMC: 1851635. DOI: 10.1093/nar/gkl1120. View

19.

Liu T, Qiao H, Wang Z, Yang X, Pan X, Yang Y . CodLncScape Provides a Self-Enriching Framework for the Systematic Collection and Exploration of Coding LncRNAs. Adv Sci (Weinh). 2024; 11(22):e2400009. PMC: 11165466. DOI: 10.1002/advs.202400009. View

20.

Chernikov I, Ponomareva U, Chernolovskaya E . Structural Modifications of siRNA Improve Its Performance In Vivo. Int J Mol Sci. 2023; 24(2). PMC: 9862127. DOI: 10.3390/ijms24020956. View