Dataset Information

DbPepNeo: a manually curated database for human tumor neoantigen peptides.

ABSTRACT: Neoantigens can function as actual antigens to facilitate tumor rejection, which play a crucial role in cancer immunology and immunotherapy. Emerging evidence revealed that neoantigens can be used to develop personalized, cancer-specific vaccines. To date, large numbers of immunogenomic peptides have been computationally predicted to be potential neoantigens. However, experimental validation remains the gold standard for potential clinical application. Experimentally validated neoantigens are rare and mostly appear scattered among scientific papers and various databases. Here, we constructed dbPepNeo, a specific database for human leukocyte antigen class I (HLA-I) binding neoantigen peptides based on mass spectrometry (MS) validation or immunoassay in human tumors. According to the verification methods of these neoantigens, the collection of peptides was classified as 295 high confidence, 247 medium confidence and 407?794 low confidence neoantigens, respectively. This can serve as a valuable resource to aid further screening for effective neoantigens, optimize a neoantigen prediction pipeline and study T-cell receptor (TCR) recognition. Three applications of dbPepNeo are shown. In summary, this work resulted in a platform to promote the screening and confirmation of potential neoantigens in cancer immunotherapy. Database URL: www.biostatistics.online/dbPepNeo/.

SUBMITTER: Tan X

PROVIDER: S-EPMC7043295 | biostudies-literature | 2020 Jan

REPOSITORIES: biostudies-literature

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dbPepNeo: a manually curated database for human tumor neoantigen peptides.

Tan Xiaoxiu X Li Daixi D Huang Pengjie P Jian Xingxing X Wan Huihui H Wang Guangzhi G Li Yuyu Y Ouyang Jian J Lin Yong Y Xie Lu L

Database : the journal of biological databases and curation 20200101

Neoantigens can function as actual antigens to facilitate tumor rejection, which play a crucial role in cancer immunology and immunotherapy. Emerging evidence revealed that neoantigens can be used to develop personalized, cancer-specific vaccines. To date, large numbers of immunogenomic peptides have been computationally predicted to be potential neoantigens. However, experimental validation remains the gold standard for potential clinical application. Experimentally validated neoantigens are ra ...[more]

PMID: 32090262

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Project description:MotivationThe interactions among various types of cells play critical roles in cell functions and the maintenance of the entire organism. While cell-cell interactions are traditionally revealed from experimental studies, recent developments in single-cell technologies combined with data mining methods have enabled computational prediction of cell-cell interactions, which have broadened our understanding of how cells work together, and have important implications in therapeutic interventions targeting cell-cell interactions for cancers and other diseases. Despite the importance, to our knowledge, there is no database for systematic documentation of high-quality cell-cell interactions at the cell type level, which hinders the development of computational approaches to identify cell-cell interactions.ResultsWe develop a publicly accessible database, CITEdb (Cell-cell InTEraction database, https://citedb.cn/), which not only facilitates interactive exploration of cell-cell interactions in specific physiological contexts (e.g. a disease or an organ) but also provides a benchmark dataset to interpret and evaluate computationally derived cell-cell interactions from different tools. CITEdb contains 728 pairs of cell-cell interactions in human that are manually curated. Each interaction is equipped with structured annotations including the physiological context, the ligand-receptor pairs that mediate the interaction, etc. Our database provides a web interface to search, visualize and download cell-cell interactions. Users can search for cell-cell interactions by selecting the physiological context of interest or specific cell types involved. CITEdb is the first attempt to catalogue cell-cell interactions at the cell type level, which is beneficial to both experimental, computational and clinical studies of cell-cell interactions.Availability and implementationCITEdb is freely available at https://citedb.cn/ and the R package implementing benchmark is available at https://github.com/shanny01/benchmark.Supplementary informationSupplementary data are available at Bioinformatics online.

Dataset Information

DbPepNeo: a manually curated database for human tumor neoantigen peptides.

Publications

dbPepNeo: a manually curated database for human tumor neoantigen peptides.

Similar Datasets

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