FAQs
Q1. What is ASPsiDb ?
ASPsiDb is an comprehensive repository of a new category of therapeutically relevant siRNAs called Allele specific siRNAs (ASP-siRNAs), which can differentiate between two alleles of a target gene even with one single nucleotide difference. Currently database contains 2594 experimentally validated Allele Specific siRNAs against 62 unique targets genes from 43 different genetic diseases reported in scientific literature till now.
Q2. How Allele discriminative-siRNAs are different from general siRNAs ?
Traditional or general siRNAs are optimized to specifically target a particular gene , but they are not usually made fine-tuned to discriminate between the two alleles of a single gene. Therefore they suppress both alleles with comparable efficacy, while “ASP-siRNAs” are designed to discriminate between the mutant allele from the wild allele of a gene, even if the mutant and wild type alleles are differed only by single nucleotide difference.
Q3. Why there is need of ASP-siRNAs ?
Genetic diseases like Neurodegenerative disorders, skin disorders, cancer, viral infections, muscular disorders, skeletal disorders etc, where mutation occurs in one allele of the gene, while the wild allele is critical for organism's survival. Therefore in order to look for a better therapeutic for these type of diseases; it should ideally do not harm wild-type allele.
Therapeutic intervention of these dominant negative genetic disorders at protein level with pharmacological drugs is challenging due to structural similarity of the normal allele of the targets from the mutant ones. Situation even worsens if the target gene contains single nucleotide polymorphism (SNP), as it will be not be discriminated by conventional drugs due to their lack of selectivity (Seyhan et.al., Hum Genet 2011; Zhang Y et.al., Nat Gene Ther 2011).
ASP-siRNAs stands very well to combat these genetic diseases in a better way as they can inhibit mutant allele sparing the wild allele. Q4. What is the importance of ASPsiDb database to scientific community ? Since, “ASP-siRNAs” have therapeutic potential to discriminate the wild and mutant alleles of a single gene, this would be amenable for the treatment of genetic diseases. Therefore, a centralized repository of ASP-siRNAs would be very helpful for scientic community. Thus, in order to make these ASP-siRNAs quickly accessible in the form of a comprehensive database; we have developed ASPsiDb.There are two implications of ASPsiDb: a) To keep all experimentally validated ASP-siRNAs/shRNAs reported in scientific literature at one stand-alone archive. b)This database will be very helpful to develop an prediction algorithm for the designing highly effective allele-specific siRNAs and might also provide guide to increase the specificity of therapeutic siRNAs by machine learning techniques. Q5. How many total entries are there in ASPsiDb ? Presently, ASPsiDb contains total of 2594 experimentally validated Allele specific siRNAs. Q6. What are the fields of ASPsiDb ? These are as follows- (i) ASP-siRNA ID (ii) ASP-siRNA name,(iii) ASP-siRNA sequence, (iv) Mismatch in ASP-siRNA with reference to wild type siRNA, (vi) ASP siRNA efficacy for mutant and wild allele, (vii) %age discrimination, (viii) Target gene name, (ix) Mutation in Target, (x)Target sequence , (xi) Uniprot id, (x) Concentration, (xi)Cell line, (xii) Experimental method, (xiii) siRNA expression method, (xiv) OMIM ID (xv) Pubmed id (xvi) Transfection method. Q7. How many target genes are there targeted by allele specific siRNAs?
Currently, there are 62 unique target genes entries; which cause a total of 43 diseases.
Q8. How many diseases are there in ASPsiDb and under how many categories it come?
There are a total of 43 different diseases; which comes under 8 categories viz 1. Neurodegenerative-disorders, 2. skin-disorders, 3. Auto-immune disorders, 4. cancer, 5. viral diseases, 6. Skeletal Disorders, 7. muscular Disorders, 8.ASP siRNA in other diseases.
Q9. How to use search option in ASPsiDb ?
User can perform search option in the following two ways:
1. User can perform a quick search by giving a keyword to the “quick search” radio button provided at the top of the web interface and click submit.
2. Second, user can enter the query/keyword after clicking search on menu bar.The user given keyword can be searched in the all fields like siRNA ID, SiRNA sequence sense, Mismatch in siRNA, Disease, Concentration, Target, Mismatch in Target, UniProt ID, Target sequence, SNP, %age discrimination, Cell line, Experimental technique, siRNA expression method, OMIM ID, PMID, Transfection method OR there is also facility that user can select some out of all fields to search that keyword in those fields only.
Q10. How to use advanced search option in ASPsiDb ?
In the ‘Advance Search’ option, the user can enter keyword and search the data using logical operators (AND/OR) to make more flexible and stringent queries.
Q11. Describe the tools incorporated in ASPsiDb and their advantage ?
We have provided two tools in ASPsiDb to help user analyze their sequence.These are :
1) ASPsiBLAST: To blast user provided siRNA to the ASP-siRNAs in the database.
2) ASPsiTarMap: To align user given target sequence on ASPsiRNAs of the database.
3)ASPsiMap:To map user given gene sequence on ASP-siRNAs in ASPsiDB.
Q12. What is the use of ASPsiBLAST tool ?
The ASPsiBLAST tool searches the siRNA sequence in the database similar to the siRNA sequence provided by the user and searches whether that siRNA sequence have been already reported in the literature or not.
Q13. What is the use of ASPsiTarMap tool ?
In ASPsiTarMap tool can be use to find out the allele specific siRNAs in the database against the user given target gene sequence.Therefore it can be helpful to use these siRNAs for the suppression of muatnt target gene without causing much suppression of wild type gene.
Q14. How to download data from ASPsiDb ?
Data is freely available to download from ASPsiDb under the downloads section in the menu bar. User can download entire database in excel format depending upon their requirement.
Q15. How to submit data in ASPsiDb ?
Experimental biologists, who are doing research in the field of are welcomed to submit their experimentally validated ASP-siRNA sequences in the database.
Q16. Is this database freely available ?
Yes , this database is freely available through this url: http://crdd.osdd.net/servers/allsidb