Open Access Highly Accessed Research article

Transcripts with in silico predicted RNA structure are enriched everywhere in the mouse brain

Stefan E Seemann12, Susan M Sunkin3, Michael J Hawrylycz3, Walter L Ruzzo145 and Jan Gorodkin12*

Author Affiliations

1 Center for non-coding RNA in Technology and Health, University of Copenhagen, Denmark

2 , IBHV, University of Copenhagen, Denmark

3 Allen Institute for Brain Science, , USA

4 Computer Science and Engineering and Genome Sciences, Univ. of Washington, USA

5 Fred Hutchinson Cancer Research Center, , USA

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BMC Genomics 2012, 13:214  doi:10.1186/1471-2164-13-214

Published: 31 May 2012

Additional files

Addtional file 1 :

Annotation of predicted structured probes. CSV-file listing the features of all structured probes from Table 1 and their CMfinder predicted RNA secondary structures.

Format: CSV Size: 16.3MB Download file

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Addtional file 2 :

Tables and figures. This file contains lists of correlated expressed structured riboprobes, and additional tables and figures.

Format: PDF Size: 919KB Download file

This file can be viewed with: Adobe Acrobat Reader

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Addtional file 3 :

GO analysis of structured UTR probes. 4115 structured UTR probes with known gene symbols are examined for GO term enrichment.

Format: TAB Size: 1MB Download file

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Addtional file 4 :

GO analysis of non-structured UTR probes. 3407 non-structured UTR probes with known gene symbols are examined for GO term enrichment.

Format: TAB Size: 408KB Download file

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Addtional file 5 :

Predicted significant RNA-RNA interactions. CSV-file listing 585 significant (p-value<1e-05) interactions between structured putative ncRNAs and UTRs. The interaction sites are predicted by RNAplfold and RNAplex to be larger than 9 nt and with a MFE smaller than -40 kcal/mol.

Format: CSV Size: 32KB Download file

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