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SPENCER: a comprehensive database for small peptides encoded by noncoding RNAs in cancer patients

As an increasing number of noncoding RNAs (ncRNAs) have been suggested to encode short bioactive peptides in cancer, the exploration of ncRNA-encoded small peptides (ncPEPs) is emerging as a fascinating field in cancer research. To assist in studies on the regulatory mechanisms of ncPEPs, we describ...

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Detalles Bibliográficos
Autores principales: Luo, Xiaotong, Huang, Yuantai, Li, Huiqin, Luo, Yihai, Zuo, Zhixiang, Ren, Jian, Xie, Yubin
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8728293/
https://www.ncbi.nlm.nih.gov/pubmed/34570216
http://dx.doi.org/10.1093/nar/gkab822
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author Luo, Xiaotong
Huang, Yuantai
Li, Huiqin
Luo, Yihai
Zuo, Zhixiang
Ren, Jian
Xie, Yubin
author_facet Luo, Xiaotong
Huang, Yuantai
Li, Huiqin
Luo, Yihai
Zuo, Zhixiang
Ren, Jian
Xie, Yubin
author_sort Luo, Xiaotong
collection PubMed
description As an increasing number of noncoding RNAs (ncRNAs) have been suggested to encode short bioactive peptides in cancer, the exploration of ncRNA-encoded small peptides (ncPEPs) is emerging as a fascinating field in cancer research. To assist in studies on the regulatory mechanisms of ncPEPs, we describe here a database called SPENCER (http://spencer.renlab.org). Currently, SPENCER has collected a total of 2806 mass spectrometry (MS) data points from 55 studies, covering 1007 tumor samples and 719 normal samples. Using an MS-based proteomics analysis pipeline, SPENCER identified 29 526 ncPEPs across 15 different cancer types. Specifically, 22 060 of these ncPEPs were experimentally validated in other studies. By comparing tumor and normal samples, the identified ncPEPs were divided into four expression groups: tumor-specific, upregulated in cancer, downregulated in cancer, and others. Additionally, since ncPEPs are potential targets for neoantigen-based cancer immunotherapy, SPENCER also predicted the immunogenicity of all the identified ncPEPs by assessing their MHC-I binding affinity, stability, and TCR recognition probability. As a result, 4497 ncPEPs curated in SPENCER were predicted to be immunogenic. Overall, SPENCER will be a useful resource for investigating cancer-associated ncPEPs and may boost further research in cancer.
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spelling pubmed-87282932022-01-05 SPENCER: a comprehensive database for small peptides encoded by noncoding RNAs in cancer patients Luo, Xiaotong Huang, Yuantai Li, Huiqin Luo, Yihai Zuo, Zhixiang Ren, Jian Xie, Yubin Nucleic Acids Res Database Issue As an increasing number of noncoding RNAs (ncRNAs) have been suggested to encode short bioactive peptides in cancer, the exploration of ncRNA-encoded small peptides (ncPEPs) is emerging as a fascinating field in cancer research. To assist in studies on the regulatory mechanisms of ncPEPs, we describe here a database called SPENCER (http://spencer.renlab.org). Currently, SPENCER has collected a total of 2806 mass spectrometry (MS) data points from 55 studies, covering 1007 tumor samples and 719 normal samples. Using an MS-based proteomics analysis pipeline, SPENCER identified 29 526 ncPEPs across 15 different cancer types. Specifically, 22 060 of these ncPEPs were experimentally validated in other studies. By comparing tumor and normal samples, the identified ncPEPs were divided into four expression groups: tumor-specific, upregulated in cancer, downregulated in cancer, and others. Additionally, since ncPEPs are potential targets for neoantigen-based cancer immunotherapy, SPENCER also predicted the immunogenicity of all the identified ncPEPs by assessing their MHC-I binding affinity, stability, and TCR recognition probability. As a result, 4497 ncPEPs curated in SPENCER were predicted to be immunogenic. Overall, SPENCER will be a useful resource for investigating cancer-associated ncPEPs and may boost further research in cancer. Oxford University Press 2021-09-27 /pmc/articles/PMC8728293/ /pubmed/34570216 http://dx.doi.org/10.1093/nar/gkab822 Text en © The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research. https://creativecommons.org/licenses/by-nc/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License (https://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Database Issue
Luo, Xiaotong
Huang, Yuantai
Li, Huiqin
Luo, Yihai
Zuo, Zhixiang
Ren, Jian
Xie, Yubin
SPENCER: a comprehensive database for small peptides encoded by noncoding RNAs in cancer patients
title SPENCER: a comprehensive database for small peptides encoded by noncoding RNAs in cancer patients
title_full SPENCER: a comprehensive database for small peptides encoded by noncoding RNAs in cancer patients
title_fullStr SPENCER: a comprehensive database for small peptides encoded by noncoding RNAs in cancer patients
title_full_unstemmed SPENCER: a comprehensive database for small peptides encoded by noncoding RNAs in cancer patients
title_short SPENCER: a comprehensive database for small peptides encoded by noncoding RNAs in cancer patients
title_sort spencer: a comprehensive database for small peptides encoded by noncoding rnas in cancer patients
topic Database Issue
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8728293/
https://www.ncbi.nlm.nih.gov/pubmed/34570216
http://dx.doi.org/10.1093/nar/gkab822
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