Small interfering RNA databases | Non-coding transcript data analysis

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 meantime, 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. The current release of siRecords contains the records of 17,192 RNAi experiments targeting 5,086 genes. Data contributors could submit their own records of RNAi experiments.

A bioinformatics resource for cereal crops consisting of large-scale datasets of maize and rice smRNA sequences generated by high-throughput pyrosequencing.

A manually curated database having comprehensive details of 1358 siRNA/shRNA targeting viral genome regions. Further, wherever available, information regarding alternative efficacies of above 300 siRNAs derived from different assays has also been incorporated. Important fields included in the database are siRNA sequence, virus subtype, target genome region, cell type, target object, experimental assay, efficacy, off-target and siRNA matching with reference viral sequences. Database also provides the users with facilities of advance search, browsing, data submission, linking to external databases and useful siRNA analysis tools especially siTarAlign which align the siRNA with reference viral genomes or user defined sequences. VIRsiRNAdb contains extensive details of siRNA/shRNA targeting 42 important human viruses including influenza virus, hepatitis B virus, HPV and SARS Corona virus. It is possible to perform a quick search based on various database fields i.e. Virus name, siRNA sequence, target region, cell line and Pubmed ID.

A manually curated database that provides comprehensive experimentally supported associations about nervous system diseases (NSDs) and noncoding RNAs (ncRNAs). NSDNA database documents 24713 associations between 142 NSDs and 8593 ncRNAs in 11 species, curated from more than 1300 articles. This database provides a user-friendly interface for browsing and searching and allows for data downloading flexibility. In addition, NSDNA offers a submission page for researchers to submit novel NSD-ncRNA associations. It represents a useful and valuable resource for researchers who seek to understand the functions and molecular mechanisms of ncRNA involved in NSDs.

Centralizes 24 nucleotide small interfering RNA (24-nt siRNA) loci and information, including fundamental locus information, expression profiles and annotation of transposon elements, from next-generation sequencing (NGS) data for 10 popular plant species. Pln24NT provides an intuitive web interface for convenient searching and browsing. Furthermore, analytical tools were included to help users flexibly analyze their own siRNA NGS data. Pln24NT will help the plant research community to discover and characterize 24-nt siRNAs, and may prove useful for studying the roles of siRNA in RNA-directed DNA methylation in plants.

Facilitates the design of vector-based small interference RNA (siRNA) and siRNA cassette. GenScript's siRNA Design Center provides second generation siRNA design tool, that consists of a siRNA target finder, a siRNA construct builder and a siRNA sequence scramble. To protect users’ privacy, the programs are hosted on a secure Web server.

A specialized databank for chemically modified siRNAs. siRNAmod contains a total of 4894 chemically modified-siRNA sequences, comprising 128 unique chemical modifications on different positions with various permutations and combinations. It incorporates important information on siRNA sequence, chemical modification, their number and respective position, structure, simplified molecular input line entry system canonical (SMILES), efficacy of modified siRNA, target gene, cell line, experimental methods, reference etc. siRNAmod browsing option helps user to surf via these five categories: i) modification in sense strand, ii) position of modification in sense strand, iii) modification in antisense strand, iv) position of modification in antisense strand and v) reference.

In silico resources developed to facilitate scientific community fighting against deadly virus EBOLA. EbolaVCR enlists possible vaccine candidates, therapeutic siRNAs and other related resources. Firstly, we predicted and identified experimentally validated epitopes in each of the antigens/proteins of the five known ebolaviruses. Secondly, we generated all the possible overlapping 9mer peptides from the proteins of ebolaviruses. Thirdly, conserved peptides across all the five ebolaviruses (four human pathogenic species) with no identical sequence in the human proteome, based on 1000 Genomes project, were identified. Finally, we identified peptide or epitope-based vaccine candidates that could activate both the B- and T-cell arms of the immune system. In addition, we also identified efficacious siRNAs against the mRNA transcriptome (absent in human transcriptome) of all the five ebolaviruses.

Provides a collection of currently available public databases with non-coding RNA information. NRDR permits users to search a list of databases filtered by user-defined criteria based on RNA family, information source, information content and search mechanisms. It enables the generation of statistics on how the databases are distributed according to each classification criterion. This database integrates data sets of regulation expression, target genes and putative regulated networks and pathways.

A manually curated database of HIV inhibiting siRNAs that provides comprehensive information about each siRNA or shRNA. HIVsirDB structure contains sixteen fields including siRNA sequence, HIV strain, targeted genome region, efficacy and conservation of target sequences. Users can explore information in user friendly manner using the search and browsing facility. HIVsirDB is useful to experimentalists in deciding the highly potent siRNAs targeting the most susceptible target site in HIV genome and its experimental procedure to suppress HIV infection.

Offers information about 2 million products, submitted by a reagent provider partners. All reagents are organized according to genes, species, reagent types (antibodies, recombinant proteins, ELISA, siRNA, cDNA clones, biochemicals, and others). VAD is developed with manually curation antibody applications from selected formal publications. Review articles for antibodies, based on VAD, and for commonly used reagents are freely available.

Aims to provide a resource for researchers looking for validated siRNAs against target genes, with an emphasis on genes potentially involved in cancer. The MIT/ICBP siRNA database has basic information regarding submitted sequences. In addition, we provide links to more annotated information available through NCBI's probe database.

Allows researchers worldwide access to information as well as allow purchase of the constructs. RNAi Codex holds data from the Hannon–Elledge shRNA library and allows the use of biologist-friendly gene names to access information on shRNA constructs that can silence the gene of interest. It is designed to hold user-contributed annotations and publications for each construct, as and when such data become available.

Provides sequences of published functional siRNA molecules targeting human genes and important technical details of the corresponding gene silencing experiments, including the mode of siRNA generation, recipient cell lines, transfection reagents and procedures and direct links to published references (PubMed). To retrieve functional siRNAs sequences for a specific gene, the human siRNA database can be searched for UniGene cluster IDs, gene names, RefSeq accession numbers and target gene descriptions.

Provides a gene-centric view of siRNA experimental data, including siRNAs of known efficacy and siRNAs predicted to be of high efficacy by a combination of methods. Linked to these sequences is information such as siRNA thermodynamic properties and the potential for sequence-specific off-target effects. The database interface was designed with the experimental user group as the primary target audience. The user interface is gene-centric, allowing the user to search by nucleotide accession number, free text, sequence or by viewing the list of genes with verified siRNAs.

Serves as a specific oligo repository of probe, siRNA and primer design for human genome. SpecificDB is based on an integration of ANN and BLAST (IAB) algorithm to predict and identify specific N-mer oligos through polymerase chain reaction experiments. The web platform also offers several tools for microarray analysis and genome-wide iterative enrichment analysis.

Hosts off-target information. SeedSeq is an online repository that aims to provide a data source for design, validation of small-interfering RNA (siRNA) libraries, and experiments. The particularity of this database is that it furnishes collection of human mRNA transcripts and their siRNA reagents off-target predictions in GenBank format. Its design permits users to determine which transcripts are the most sensitive for being off-target.

Provides a siRNA oligonucleotide data from different sources and companies, and visualize interactions between siRNA oligo and predicted off-target.

Contains information about small interference (siRNAs) targeted at human oncogenes. DSTHO is an online database that allows screening of human oncogenes (OsiRNA) sequences according to the sequence motifs and positional preference of the nucleotide bases. In summary, this database is designed to aid the synthesis of siRNAs, which target OsiRNAs.