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Targetscan.org Edit

Micro RNA's (miR's) are 19-22 long nucleotide long non coding RNA molecules that are produced endogenously in cells, they are involved in post transcriptional regulation of gene expression by binding to their target mRNA at the complimetary sites and result in the degration or translational inhibition of target mRNA[1]. Recent research elutes the role of miR's in cancers, autoimmune diseases, neurological disease[2], development etc. 

Recently few web based databases for miRs have emereged which enable to predict the targets for miR's which researchers are interested in and also predict miR's that could target the gene of interest. One such database is targetscan.org. Targetscan enables you to search for predicted miRs that target your gene of interest or search for targets a particular miR or family of miR's. Researchers do update the database based on their expanded research and contribute to the database frequently[3].

HistoryEdit

The target scan tool is started and maintained by the Whitehead Institute and Bioinformatics and Research Computing from 2006 - present. 

UtilityEdit

TargetScan enables miRNA target predicition by searching for 7mer -8mers  that match the seed regions on the RNA.The predictions are ranked based on the context+ scores of the sites and  by the probability of site conservation.

TutorialEdit

1) Select the species from dropdown box.

2) Enter the ENTREZ gene symbol.

3) Select if you want to search for broadly conserved miR. (Conserved in humans, mouse, rats etc) or narrowly conserved (humans only, mouse only etc).

Target scan1

If you have a family of miRs or a specific miR in mind you could use them to refine your search.

4) Submit your query.

5) Then the algorithm searches and displays the accession numbers of the transcripts it finds for the gene you searched for, click on the transcript you are interested in.

6) A new tab opens with list of predicted miR's,the top prediticted sites are listed in descentidng ordre of the context positive scores.

Target scan2

7) Click on the miR to get further information and its litreature citations.

Section headingEdit

1.            Bushati N & Cohen SM (2007) microRNA functions. Annual review of cell 'and developmental biology 23:175-205.

2.            Schaefer A, et al. (2007) Cerebellar neurodegeneration in the absence of microRNAs. The Journal of experimental medicine 204(7):1553-1558.

3.            Friedman RC, Farh KK, Burge CB, & Bartel DP (2009) Most mammalian mRNAs are conserved targets of microRNAs. Genome research 19(1):92-105.