Evidence map›Paper›PMID 35493528›Full record

ArticleFrontiers in immunology2022

dbPepNeo2.0: A Database for Human Tumor Neoantigen Peptides From Mass Spectrometry and TCR Recognition.

Manman Lu, Linfeng Xu, Xingxing Jian, Xiaoxiu Tan, Jingjing Zhao, Zhenhao Liu, Yu Zhang, Chunyu Liu, Lanming Chen, Yong Lin and 1 more

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Frontiers in immunology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers, 1 of them a synthesis that pooled it.

0numbers the graph read from it
0cells of the map it votes in
24citing papers in PubMed, 1 pooled it
2.6field-weighted citation impact, top 9% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

24 citing papers in PubMed, 1 synthesis or guideline pooled it, 31 citations in OpenAlex.

  1. Pooled it
  2. Technical review of artificial intelligence in TCR-T therapy.Journal of the National Cancer Center · 2026
    Review
  3. Article
  4. Article
  5. Article
  6. Article
  7. Article
  8. Review
  9. Article
  10. [Prediction of MHC II antigen peptide-T cell receptors binding based on foundation model].Sheng wu yi xue gong cheng xue za zhi = Journal of biomedical engineering = Shengwu yixue gongchengxue zazhi · 2024
    Article
  11. Review
  12. Review
  13. Review
  14. Review
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  16. Review
  17. Neodb: a comprehensive neoantigen database and discovery platform for cancer immunotherapy.Database : the journal of biological databases and curation · 2023
    Article
  18. Article
  19. Article
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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

11 authors at 4 institutions in 1 country.

Manman LuCollege of Food Science and Technology, Shanghai Ocean University, Shanghai, China.
Linfeng XuShanghai-Ministry of Science and Technology (MOST) Key Laboratory of Health and Disease Genomics, Institute for Genome and Bioinformatics, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, China.
Xingxing JianShanghai-Ministry of Science and Technology (MOST) Key Laboratory of Health and Disease Genomics, Institute for Genome and Bioinformatics, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, China.
Xiaoxiu TanShanghai-Ministry of Science and Technology (MOST) Key Laboratory of Health and Disease Genomics, Institute for Genome and Bioinformatics, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, China.
Jingjing ZhaoCollege of Food Science and Technology, Shanghai Ocean University, Shanghai, China.
Zhenhao LiuShanghai-Ministry of Science and Technology (MOST) Key Laboratory of Health and Disease Genomics, Institute for Genome and Bioinformatics, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, China.
Yu ZhangShanghai-Ministry of Science and Technology (MOST) Key Laboratory of Health and Disease Genomics, Institute for Genome and Bioinformatics, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, China.
Chunyu LiuCollege of Food Science and Technology, Shanghai Ocean University, Shanghai, China.
Lanming ChenCollege of Food Science and Technology, Shanghai Ocean University, Shanghai, China.
Yong LinSchool of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, China.
Lu XieCollege of Food Science and Technology, Shanghai Ocean University, Shanghai, China.
Shanghai Ocean University · CNUniversity of Shanghai for Science and Technology · CNShanghai Jiao Tong University · CNXiangya Hospital Central South University · CN

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Neoantigens are widely reported to induce T-cell response and lead to tumor regression, indicating a promising potential to immunotherapy. Previously, we constructed an open-access database, i.e., dbPepNeo, providing a systematic resource for human tumor neoantigens to storage and query. In order to expand data volume and application scope, we updated dbPepNeo to version 2.0 (http://www.biostatistics.online/dbPepNeo2). Here, we provide about 801 high-confidence (HC) neoantigens (increased by 170%) and 842,289 low-confidence (LC) HLA immunopeptidomes (increased by 107%). Notably, 55 class II HC neoantigens and 630 neoantigen-reactive T-cell receptor-β (TCRβ) sequences were firstly included. Besides, two new analytical tools are developed, DeepCNN-Ineo and BLASTdb. DeepCNN-Ineo predicts the immunogenicity of class I neoantigens, and BLASTdb performs local alignments to look for sequence similarities in dbPepNeo2.0. Meanwhile, the web features and interface have been greatly improved and enhanced.

Indexed as

Antigens, NeoplasmNeoplasmsHumansMass SpectrometryPeptidesReceptors, Antigen, T-Cell, alpha-betaAntigens, NeoplasmPeptidesReceptors, Antigen, T-Cell, alpha-betadeep learningexperimental validationmass spectrometryneoantigenTCR

Identifiers

PMID35493528
PMCPMC9043652
OpenAlexW4224132465

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.