Quantitative predictions of protein interactions with long non-coding RNAs
Abstract
Long noncoding RNAs (lncRNAs, which comprise 68% of the human transcriptome with average length of 1,000 nt) interact with various RNA-binding proteins (RBPs) to mediate cellular functions1. Identification of lncRNA interactions through experimental methods is challenging and can be complemented by the use of computational models to predict protein partners. Yet it is currently impractical to calculate RBP–lncRNA interactions for large transcripts2.We introduce Global Score as a means to predict protein interactions with large RNAs (http://service.tartaglialab.com/new_submission/globalscore).
Additional Information
© 2017 Macmillan Publishers Limited. Published online 29 December 2016. We thank D. Whitworth and K. Havas for critical reading of the manuscript, the European Research Council (RIBOMYLOME_309545), MINECO (BFU2014-55054-P), Centro de Excelencia Severo Ochoa 2013–2017, and the European Molecular Biology Laboratory Grant-50800. Data availability. The webserver, documentation, and compiled stand-alone version of Global Score are available at http://service.tartaglialab.com/new_submission/globalscore. Data from HnrnpK, Ptbp1, Lbr, HnrnpU, Sharp, and Dkc1 eCLIP experiments are deposited at the GEO with codes (respectively) GSM2325771, GSM2299086, GSM2299085, GSM2325772, GSM2299084, and GSM2325770. The authors declare no competing financial interests.Attached Files
Supplemental Material - nmeth.4100-S1.pdf
Supplemental Material - nmeth.4100-S2.xlsx
Supplemental Material - nmeth.4100-S3.xlsx
Supplemental Material - nmeth.4100-S4.xlsx
Supplemental Material - nmeth.4100-S5.xlsx
Supplemental Material - nmeth.4100-S6.xlsx
Supplemental Material - nmeth.4100-SF1.jpg
Supplemental Material - nmeth.4100-SF2.jpg
Supplemental Material - nmeth.4100-SF3.jpg
Supplemental Material - nmeth.4100-SF4.jpg
Supplemental Material - nmeth.4100-SF5.jpg
Supplemental Material - nmeth.4100-SF6.jpg
Supplemental Material - nmeth.4100-SF7.jpg
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Additional details
- Eprint ID
- 71504
- DOI
- 10.1038/nmeth.4100
- Resolver ID
- CaltechAUTHORS:20161026-132024065
- European Research Council (ERC)
- RIBOMYLOME_309545
- Ministerio de EconomÃa, Industria y Competitividad (MINECO)
- BFU2014-55054-P
- Centro de Excelencia Severo Ochoa
- European Molecular Biology Laboratory (EMBL)
- 50800
- Created
-
2017-01-03Created from EPrint's datestamp field
- Updated
-
2021-11-11Created from EPrint's last_modified field