Frequently Asked Questions

Q. What is saRNA?

saRNA stands for small activating RNA, recently discovered phenomenon related to RNA activation (RNAa) that involves use of small double stranded RNA 19 t0 21 nucleotide long (similar to siRNA but different in mechanism and results) and activates the gene expression.
This webserver saRNAdb, is a manually curated database for experimentally validated small activating RNAs and the proteins involved.


Q. How is the promoter sequence and gene sequence provided in database and their relation to saRNA displayed? 

The promoter and gene infomration has been extracted from Eukaryotic Promoter database (EPD) and is represented as fasta sequence/file. We have used the same notation as used in EPD with small letters representing the promoter sequence and gene sequence with capital letters distinguished at Transcriptional start site (TSS) downstream. Furthermore, the promoter sequence is -10000 base pair upstream and gene sequence is provided as per the information on length provided in genecards down stream of TSS. Furthermore, we have calculated the positions of the alignment of the saRNAs and also displayed it in jbrowse. Following figure shows how the calculations have been made to represent the alignment of saRNA with Promoter with respect to promoter (10000 base pair) and Transcriptioanl start site.


Q. why was promoter sequence length chosen upto 10000 base pair and not less or more? 

Data analysis showed that the maximum upstream position of saRNA target was around 9800 base pair from transcription start site. Furthermore, there is no defined length of the promoter as such so we fixed the promoter length arbitrarily to 10000 base pair.
Q. How to find information about the proteins involved in saRNA phenomena?

We have provided curated list of proteins that are involved in RNA activation process. We have curated and provided the visual tool; cytoscape to display these proteins and their interacting partners. They are also linked to the external information sources of GeneCards and UniProtkb , the information can be acessed through this url: http://bioinfo.imtech.res.in/manojk/sarna/proteins.php


Q. What is the importance of saRNA platform to scientific community?

saRNA phenomena is the recent field discovered in 2006-07 and has been showen to be promising in various diseases/conditions like various cancers, cell cycle, apoptosis, hypoxia, brain abnormalities, differentiation, cell membrane transporters, erectile dysfunction, inflammation, preclampsia, stem cells. A compny namely MiNA Therapeutics is working on saRNA therapeutics development, seeing the promising nature of the saRNAs.


Q. How many total entries are there in saRNAdb ?

The total number of saRNA sequences in the database are 2150 entries that include their detailed information like reference ID, cell line used experiments used, chemical modification(s) and their position(s) predicted secondary structures and MFE (minimum free energy by RNAfold) of both sense and antisense and in combination of both these. Besides we have provided the design rules for designing of saRNAs. We have included the information about the proteins involved in the saRNA mechanism.


Q. What are the fields of saRNA database?

The follows are the fields in the database: -

(I) Information form the paper Name as in paper, Sequence both sense antisense, Length of both strands, 3-Ends Modification(s), Position of modification(s), Sequence (promoter and gene), Activity qualitative and quantitative, Expression (Unit), Cell line used in this query, Experiment used, Concentration used, Other experiments used in study, Cells or Organism used in study, Transfection method, Transfection duration, Document type, Article title, Journal information, Author information, Abstract, Reference.
(II) Information linked to other resources Target gene symbol, Target gene name, RefSeq, GeneBank, Genecards, UCSC browser, UniProtKB.
(III) Information calculated using software(s) Secondary structure both sense antisense individually, Minimum free energy (kcal/mol) both sense antisense individually, Delta-G binding (dsRNA) for sense/antisense, Secondary structure dsRNA-I sense-antisense double strand, Minimum free energy (kcal/mol) dsRNA-I, Secondary structure dsRNA-II sense-antisense double strand, Minimum free energy (kcal/mol) dsRNA-II, Alignment of the saRNA with Promoter upstream of Transcription start site (TSS), its visualization in jbrowse.


Q. What type experiments are used in saRNA to check their activity?

Mainly RNA analysis and protein analysis has been used in terms of experimentation for the saRNA analysis with Quantitative Real-time PCR and western blotting as main techniques used.


Q. What are modifications of saRNAs in database?

Mainly the modification used in the saRNAs is the deoxy thymidine in RNA molecules especially at the 3- End at positions 20 and 21 which act as 2 nucleotide overhangs. Besides 2-O-Methyl modification and 2-O-Flouro modifications have also been tested. Occassionally some conjugates like biotin etc. have also been used.


Q. How to look for infomation in the database?

Two methods can be used (I) Browse (II) Search option
(I) Browse:- if user is new to saRNA field click on the Browse option and it will display the Condition Studied, Target Gene, Cell line, Reference - Study Title.
(II) Search option User can enter the query/keyword after clicking "Search" web page on menu bar. The keyword can be searched in the all fields like Reference, Condition studied, Target gene, Experiment used, Cell line used, Transfection method used, saRNA concentration used, Time of saRNA treatment etc.
Advanced search can also be used to search using "AND" and "OR" operators and narrow down the desired query


Q. What are the tool used in this webserver ?

Two tools are provided that are helpful in database exploration of saRNAs and help user analyze their sequence. These are:

(I) saRNAdb Blast: This tool helps to blast the user provided saRNA sequences to look inside this database for their presence.
(II) saRNAdb Map: Map-tools helps to find the saRNAs from the database to user provided sequence and checks for the presenece of saRNAs in the databse that are matching with its segments anywhere.



Q. How to download data from saRNAdb? 

Data is freely available to download from saRNAdb under the downloads section in the menu bar. User can download entire database in excel or CSV format depending upon their requirement.



Q. When will be the saRNAdb updated? 

the databse will be updated anually or when ever enough data will be found available.



Q. Is this database freely available and include user login or registration?

Yes, this database is freely available and does not involve any user login or registration and can be acessed through this url: http://bioinfo.imtech.res.in/manojk/sarna/

 

saRNA - small activating RNA