Protein Lounge siRNA Database

Category Cross-Omics>Knowledge Bases/Databases/Tools

Abstract The siRNA Database is a comprehensive siRNA database that contains siRNA targets against all known mRNA sequences throughout a variety of organisms.

The database has also been subdivided into folders for siRNA against Kinases, Phosphatases, Transcription Factors and Disease genes in order to provide a total solution for your RNAi research needs.

All siRNA targets in the database are linked to Protein Lounge’s web-based siRNA cloning tool (see G6G Abstract Number 20195R) that allows users to chose from a wide variety of vectors and also search for specific repeat patterns in complete genomes.

The siRNA Database will save you a great deal of time in researching, since targets against all known genes have been pre-generated in this database, simply search for your genes and get the siRNA targets.

All genes in the siRNA database are also linked to Protein Lounge’s Protein Database (available at the manufacturer’s home page) and Protein Lounge’s Pathway Database (available at the manufacturer’s home page), giving you detailed information about the genes which the siRNA target.

This is a necessary database for anyone working with gene expression analysis and high-throughput screening.

Note: Small interfering RNAs (siRNA) represent a true breakthrough technology by which gene expression can be selectively silenced. dsRNA (double-stranded RNA) that are homologous in sequence to a gene's mRNA when introduced inside a cell suppress that gene’s expression through a process known as RNAi (RNA interference).

The basic mechanism behind RNAi is the breaking of a dsRNA matching a specific gene sequence into short pieces of siRNA.

Parameters --

The parameters for the siRNA Database are based on the methods developed for siRNA prediction by Dr. Thomas Tuschl (Max-Planck Institute).

BEST TARGET: The ‘Best Target’ for siRNA is nearest to the mRNA start sequence. Those siRNA targets which are nearest to the start sequence produce a better ‘Knock-Down’ due to cleavage of a great segment of the mRNA.

All siRNA targets have been screened to remove any siRNA which shares homology with other sequences, thus producing targets which are specific to the gene of interest.

Validation Method --

The siRNA targets which are listed in the Protein Lounge siRNA database have been statistically validated, which means that the manufacturer has tested many of the targets which have been generated in the database through experimental methods to see if these targets ‘knocked-down’ mRNA levels.

In many cases the siRNA was able to produce a knock-down of ~99%.

Additional features/capabilities include:

1) Disease Gene siRNA -- Disease list is linked to the proteins which cause them and the siRNA for those proteins.

2) Transcription Factors siRNA -- Transcription Factors are arranged by binding sites, tissue specificity and siRNA targets.

3) Kinase/Phosphatase siRNA -- Complete list of kinases/phosphatases and their siRNA targets.

Organisms include --

1) Homo sapiens - 22,864 Genes with 77,378 siRNA Targets.

2) Mus musculus - 41,192 Genes with 130,463 siRNA Targets.

3) Rattus norvegicus - 19,489 Genes with 70,394 siRNA Targets.

4) Bos taurus - 1,192 Genes with 4,037 siRNA Targets.

5) Danio rerio - 1,152 Genes with 4,498 siRNA Targets.

6) Drosophila melanogaster - 17,941 Genes with 66,240 siRNA Targets.

7) Anopheles gambiae - 15,762 Genes with 49,237 siRNA Targets.

8) Caenorhabditis elegans - 15,694 Genes with 62,448 siRNA Targets.

9) Arabidopsis thaliana - 15,491 Genes with 63,359 siRNA Targets.

10) Saccharomyces cerevisiae - 5,721 Genes with 25,378 siRNA Targets.

System Requirements

Contact manufacturer.


Manufacturer Web Site Protein Lounge siRNA Database and Protein Lounge Home

Price Contact manufacturer.

G6G Abstract Number 20191R

G6G Manufacturer Number 102215