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DoRiNA 2.0--upgrading the doRiNA database of RNA interactions in post-transcriptional regulation.

Blin K, Dieterich C, Wurmus R, Rajewsky N, Landthaler M, Akalin A - Nucleic Acids Res. (2014)

Bottom Line: To enable the inclusion of doRiNA into third-party analysis pipelines, all operations are accessible via a REST API.Alternatively, local installations can be queried using a Python API.Both the web application and the APIs are available under an OSI-approved Open Source license that allows research and commercial access and re-use.

View Article: PubMed Central - PubMed

Affiliation: Computational RNA Biology Group, Max Planck Institute for Biology of Ageing, 50931 Cologne, Germany.

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Complex search results for Srsf1 XOR Srsf2 binding.
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Figure 3: Complex search results for Srsf1 XOR Srsf2 binding.

Mentions: The serine/arginine-rich proteins (SR proteins) are RNA-binding proteins that are associated with alternative splicing, and recent findings suggest that they are involved in both exon skipping and inclusion events (18). Furthermore, Pandit et al. suggest although Srsf1 and Srsf2 binding sites largely target the same exons, certain exons are regulated by only one of the two factors, such that there is mutually exclusive binding of Srsf1 or Srsf2. Exactly these exons can be easily identified with the help of doRiNA 2.0 (see Figure 2). First of all, we select Mouse mm9 as assembly of interest. Second, we select the Srsf1 HITS-CLIP experiment into ‘set A’ and the Srsf2 experiment into ‘set B’. Moreover, we limit the search region to CDS exons using the ‘Look for binding sites in region:’ pane. Lastly, we combine the two regulator sets using the XOR set operation for mutual exclusive binding. This query yields 44 376 sites, which could be redundant for overlapping transcripts, yet are either bound by Srsf1 (19 754 sites) or Srsf2 (24 622 sites) but not by both (see Figure 3).


DoRiNA 2.0--upgrading the doRiNA database of RNA interactions in post-transcriptional regulation.

Blin K, Dieterich C, Wurmus R, Rajewsky N, Landthaler M, Akalin A - Nucleic Acids Res. (2014)

Complex search results for Srsf1 XOR Srsf2 binding.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4383974&req=5

Figure 3: Complex search results for Srsf1 XOR Srsf2 binding.
Mentions: The serine/arginine-rich proteins (SR proteins) are RNA-binding proteins that are associated with alternative splicing, and recent findings suggest that they are involved in both exon skipping and inclusion events (18). Furthermore, Pandit et al. suggest although Srsf1 and Srsf2 binding sites largely target the same exons, certain exons are regulated by only one of the two factors, such that there is mutually exclusive binding of Srsf1 or Srsf2. Exactly these exons can be easily identified with the help of doRiNA 2.0 (see Figure 2). First of all, we select Mouse mm9 as assembly of interest. Second, we select the Srsf1 HITS-CLIP experiment into ‘set A’ and the Srsf2 experiment into ‘set B’. Moreover, we limit the search region to CDS exons using the ‘Look for binding sites in region:’ pane. Lastly, we combine the two regulator sets using the XOR set operation for mutual exclusive binding. This query yields 44 376 sites, which could be redundant for overlapping transcripts, yet are either bound by Srsf1 (19 754 sites) or Srsf2 (24 622 sites) but not by both (see Figure 3).

Bottom Line: To enable the inclusion of doRiNA into third-party analysis pipelines, all operations are accessible via a REST API.Alternatively, local installations can be queried using a Python API.Both the web application and the APIs are available under an OSI-approved Open Source license that allows research and commercial access and re-use.

View Article: PubMed Central - PubMed

Affiliation: Computational RNA Biology Group, Max Planck Institute for Biology of Ageing, 50931 Cologne, Germany.

Show MeSH