sORFs.org : a repository of small ORFs identified by ribosome profiling
- Author
- Volodimir Olexiouk (UGent) , Jeroen Crappé (UGent) , Steven Verbruggen (UGent) , Kenneth Verheggen (UGent) , Lennart Martens (UGent) and Gerben Menschaert (UGent)
- Organization
- Abstract
- With the advent of ribosome profiling, a next generation sequencing technique providing a ‘snap-shot’ of translated mRNA in a cell, many short open reading frames (sORFs) with were identified. Follow-up studies revealed the existence of functional peptides, so-called micropeptides, translated from these ‘sORFs’, indicating a new class of bio-active peptides. Over the last few years, several micropeptides exhibiting important cellular functions were discovered. However, ribosome occupancy does not necessarily imply an actual function of the translated peptide, leading to the development of various tools assessing the coding potential of sORFs. Here, we introduce sORFs.org (http://www.sorfs.org), a novel database for sORFs identified using ribosome profiling. Starting from ribosome profiling, sORFs.org identifies sORFs, incorporates state-of-the-art tools and metrics and stores results in a public database. Two query interfaces are provided, a default one enabling quick lookup of sORFs and a BioMart interface providing advanced query and export possibilities. At present, sORFs.org harbors 263 354 sORFs that demonstrate ribosome occupancy, originating from three different cell lines: HCT116 (human), E14_mESC (mouse) and S2 (fruit fly). sORFs.org aims to provide an extensive sORFs database accessible to researchers with limited bioinformatics knowledge, thus enabling easy integration into personal projects.
- Keywords
- PRIDE, PEPTIDES, TRANSLATION, IN-VIVO, NUCLEOTIDE RESOLUTION, OPEN READING FRAMES, micropeptide, smorf, small open reading frame, sorf, ribosome profiling, UCSC GENOME BROWSER, RIBO-SEQ, CONSERVATION, UNIPROT, DATABASE
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Citation
Please use this url to cite or link to this publication: http://hdl.handle.net/1854/LU-6974248
- MLA
- Olexiouk, Volodimir, et al. “SORFs.Org : A Repository of Small ORFs Identified by Ribosome Profiling.” NUCLEIC ACIDS RESEARCH, vol. 44, no. D1, 2015, pp. D324–29, doi:10.1093/nar/gkv1175.
- APA
- Olexiouk, V., Crappé, J., Verbruggen, S., Verheggen, K., Martens, L., & Menschaert, G. (2015). sORFs.org : a repository of small ORFs identified by ribosome profiling. NUCLEIC ACIDS RESEARCH, 44(D1), D324–D329. https://doi.org/10.1093/nar/gkv1175
- Chicago author-date
- Olexiouk, Volodimir, Jeroen Crappé, Steven Verbruggen, Kenneth Verheggen, Lennart Martens, and Gerben Menschaert. 2015. “SORFs.Org : A Repository of Small ORFs Identified by Ribosome Profiling.” NUCLEIC ACIDS RESEARCH 44 (D1): D324–29. https://doi.org/10.1093/nar/gkv1175.
- Chicago author-date (all authors)
- Olexiouk, Volodimir, Jeroen Crappé, Steven Verbruggen, Kenneth Verheggen, Lennart Martens, and Gerben Menschaert. 2015. “SORFs.Org : A Repository of Small ORFs Identified by Ribosome Profiling.” NUCLEIC ACIDS RESEARCH 44 (D1): D324–D329. doi:10.1093/nar/gkv1175.
- Vancouver
- 1.Olexiouk V, Crappé J, Verbruggen S, Verheggen K, Martens L, Menschaert G. sORFs.org : a repository of small ORFs identified by ribosome profiling. NUCLEIC ACIDS RESEARCH. 2015;44(D1):D324–9.
- IEEE
- [1]V. Olexiouk, J. Crappé, S. Verbruggen, K. Verheggen, L. Martens, and G. Menschaert, “sORFs.org : a repository of small ORFs identified by ribosome profiling,” NUCLEIC ACIDS RESEARCH, vol. 44, no. D1, pp. D324–D329, 2015.
@article{6974248,
abstract = {{With the advent of ribosome profiling, a next generation sequencing technique providing a ‘snap-shot’ of translated mRNA in a cell, many short open reading frames (sORFs) with were identified. Follow-up studies revealed the existence of functional peptides, so-called micropeptides, translated from these ‘sORFs’, indicating a new class of bio-active peptides. Over the last few years, several micropeptides exhibiting important cellular functions were discovered. However, ribosome occupancy does not necessarily imply an actual function of the translated peptide, leading to the development of various tools assessing the coding potential of sORFs. Here, we introduce sORFs.org (http://www.sorfs.org), a novel database for sORFs identified using ribosome profiling. Starting from ribosome profiling, sORFs.org identifies sORFs, incorporates state-of-the-art tools and metrics and stores results in a public database. Two query interfaces are provided, a default one enabling quick lookup of sORFs and a BioMart interface providing advanced query and export possibilities. At present, sORFs.org harbors 263 354 sORFs that demonstrate ribosome occupancy, originating from three different cell lines: HCT116 (human), E14_mESC (mouse) and S2 (fruit fly). sORFs.org aims to provide an extensive sORFs database accessible to researchers with limited bioinformatics knowledge, thus enabling easy integration into personal projects.}},
author = {{Olexiouk, Volodimir and Crappé, Jeroen and Verbruggen, Steven and Verheggen, Kenneth and Martens, Lennart and Menschaert, Gerben}},
issn = {{0305-1048}},
journal = {{NUCLEIC ACIDS RESEARCH}},
keywords = {{PRIDE,PEPTIDES,TRANSLATION,IN-VIVO,NUCLEOTIDE RESOLUTION,OPEN READING FRAMES,micropeptide,smorf,small open reading frame,sorf,ribosome profiling,UCSC GENOME BROWSER,RIBO-SEQ,CONSERVATION,UNIPROT,DATABASE}},
language = {{eng}},
number = {{D1}},
pages = {{D324--D329}},
title = {{sORFs.org : a repository of small ORFs identified by ribosome profiling}},
url = {{http://doi.org/10.1093/nar/gkv1175}},
volume = {{44}},
year = {{2015}},
}
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