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clade: genome: assembly:


If you want to directly access the MDC internal version of the UCSC Genome-Browser click here.

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  Latest News  
2013-01-30Added a new "proximity search" feature

To add a new layer of functionality to doRiNA, we have implemented a search for positionally overlapping features (e.g. miRNA sites that overlap a known AGO site) or features having a user-defined maximal distance. The feature is accessibly by clicking the "proximity search" checkbox in step 3 of the doRiNA search interface. For a more detailed description see here.

2013-01-09Added new PAR-CLIP data from Sievers et al. 2012 and experimental descriptions into the frontend

As a new feature, full experimental descriptions are now shown as tooltips when scrolling over the list of experiments. If undesired, this feature can be switched off.

In addition, we added new PAR-CLIP data for MOV10 to our database:

Sievers C, Schlumpf T, Sawarkar R, Comoglio F, Paro R.
Mixture models and wavelet transforms reveal high confidence RNA-protein interaction sites in MOV10 PAR-CLIP data.
Nucleic Acids Res. 2012 Nov 1;40(20):e160. doi:10.1093/nar/gks697.

2012-12-21Major update of the doRiNA database including new experiments and PicTar2 predictions

We performed a major update of our database, which included the following: If you're expeciencing any unexpected behaviour, please try to reload the doRiNA website to clear the browsers cache.
2012-08-13Added hg19 support and updated PicTar predictions for ce6, mm9 and dm3.

To assign RBP binding sites in hg19, we reanalyzed the PAR-CLIP experiments from Hafner et al. and Lebedeva et al. and lifted the rest from hg18. In addition, PicTar predictions for ce6, mm9 and dm3 were updated based on mirBase v18. The corresponding update for the human PicTar predictions will follow soon.
2012-05-23Added new FET protein family PAR-CLIP data from Hoell et al. 2011 for ESWR1, FUS, TAF15 and FUS mutants

Hoell JI, Larsson E, Runge S, Nusbaum JD, Duggimpudi S, Farazi TA, Hafner M, Borkhardt A, Sander C, Tuschl T.
RNA targets of wild-type and mutant FET family proteins.
Nat Struct Mol Biol. 2011 Nov 13;18(12):1428-31. doi: 10.1038/nsmb.2163.

Union/intersection tracks for FET family proteins (excluding the mutants) have been added.
2012-02-29New aggregated tracks have been released on the doRiNA site

These consist of the union or intersection between CLIP regions present in several experiments. For the union, all regions were combined. For the intersection, only those genomic regions that are spanned by CLIP regions from all included experiments were retained. These new tracks allow even more sophisticated refinement of sites of interest (e.g. all miRNA sites included in any of the incorporated AGO-CLIPs) especially when using the combinatorial search option.

The newly included aggregate tracks are:
  • Union of all CLIP experiments integrated into doRiNA
  • Union and intersection tracks of Ago (human, mouse), Elavl1 (human) and Gld1 (c. elegans)
2011-11-15doRiNA manuscript went online
  Acknowledgements  

This project is a collaboration of many scientists at the BIMSB:

Gerd Anders developed the database with help from Marvin Jens, Minnie Fang, Sebastian Mackowiak, Andranik Ivanov, Jonas Maaskola, and Robin Graf who developed the computational pipeline for analyzing PAR-CLIP experiments. This analysis pipeline will be published elsewehere. Sebastian Mackowiak updated PicTar.

The project is jointly supervised by Christoph Dieterich (database), Markus Landthaler (PAR-CLIP), and Nikolaus Rajewsky (PAR-CLIP analysis pipeline, PicTar).

  General Info  

doRiNA is being developed at the Berlin Institute for Medical Systems Biology (BIMSB) by the group "Bioinformatics in Quantitative Biology" (group leader: Christoph Dieterich).

We kindly ask users to cite the following reference if they include doRiNA results in their manuscripts:

Anders G, Mackowiak SD, Jens M, Maaskola J, Kuntzagk A, Rajewsky N, Landthaler M, Dieterich C.
doRiNA: a database of RNA interactions in post-transcriptional regulation.
Nucleic Acids Res. 2012 Jan;40(Database issue):D180-6. Epub 2011 Nov 15.

What's New? We added a new functionality to search for locally overlapping features called "proximity search". (Latest News...)
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