ArticleNucleic acids research2022
SPENCER: a comprehensive database for small peptides encoded by noncoding RNAs in cancer patients.
Article in Nucleic acids research, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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37 citing papers in PubMed, 61 citations in OpenAlex.
- Noncoding RNA encoded peptides in tumors from discovery to mechanism and clinical translation.iScience · 2026Review
- SPAID: a comprehensive database for disease-specific autoantigens in autoimmune disorders.Advanced biotechnology · 2026Article
- Benchmarking reveals the superiority of nucleic acid foundation models in predicting lncRNA coding potential.Genome biology · 2026Article
- Computational identification and characterization of noncoding RNA-encoded peptides: tools, databases, and in silico strategies.Amino acids · 2026Review
- Recent advances in structural and functional diversities of cancer lncRNA-encoded peptides: current opportunities and challenges for enhancing cancer diagnosis and treatment.Cancer cell international · 2026Review
- Identification and Characterization of Microproteins/ MicroORFs.Methods in molecular biology (Clifton, N.J.) · 2026Article
- HGCPep: Hypergraph Deep Learning Identifies Cancer-associated Non-coding Peptides.Genomics, proteomics & bioinformatics · 2025Article
- Proteomic Profiling of Pre- and Post-Surgery Saliva of Glioblastoma Patients II: A Preliminary Investigation of the Complementary Low Molecular Mass Fraction.International journal of molecular sciences · 2025Article
- LINC00654 promotes ovarian cancer progression by facilitating nuclear export of HuR and stabilizing oncogenic mRNAs.Oncogene · 2025Article
- Characterization of Tumor Antigens from Multi-omics Data: Computational Approaches and Resources.Genomics, proteomics & bioinformatics · 2025Review
- Rational Design of a Multi-epitope Vaccine Using Neoantigen Against Colorectal Cancer Through Structural Immunoinformatics and ML-Enabled Simulation Approach.Molecular biotechnology · 2025Article
- Proteomic Analysis of the Low Molecular Mass Fraction of Newly Diagnosed and Recurrent Glioblastoma CUSA Fluid: A Pilot Investigation of the Peptidomic Profile.International journal of molecular sciences · 2025Article
- Comprehensive discovery and functional characterization of the noncanonical proteome.Cell research · 2025Article
- Noncoding RNA-encoded peptides in cancer: biological functions, posttranslational modifications and therapeutic potential.Journal of hematology & oncology · 2025Review
- Review
- Micropeptides Encoded by Noncoding RNAs: Biological Functions and Roles in Diseases.Research (Washington, D.C.) · 2025Review
- Unlocking the secrets of the immunopeptidome: MHC molecules, ncRNA peptides, and vesicles in immune response.Frontiers in immunology · 2025Review
- AthRiboNC: an Arabidopsis database for ncRNAs with coding potential revealed from ribosome profiling.Database : the journal of biological databases and curation · 2024Article
- Long non-coding RNA-encoded micropeptides: functions, mechanisms and implications.Cell death discovery · 2024Review
- HMPA: a pioneering framework for the noncanonical peptidome from discovery to functional insights.Briefings in bioinformatics · 2024Article
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Authors and funding
7 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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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