dbPepNeo2.0: A Database for Human Tumor Neoantigen Peptides From Mass Spectrometry and TCR Recognition
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...
| Main Authors: | , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2022-04-01
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| Series: | Frontiers in Immunology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fimmu.2022.855976/full |
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| author | Manman Lu Manman Lu Linfeng Xu Linfeng Xu Xingxing Jian Xingxing Jian Xiaoxiu Tan Xiaoxiu Tan Jingjing Zhao Jingjing Zhao Zhenhao Liu Yu Zhang Yu Zhang Chunyu Liu Chunyu Liu Lanming Chen Yong Lin Lu Xie Lu Xie Lu Xie |
| author_facet | Manman Lu Manman Lu Linfeng Xu Linfeng Xu Xingxing Jian Xingxing Jian Xiaoxiu Tan Xiaoxiu Tan Jingjing Zhao Jingjing Zhao Zhenhao Liu Yu Zhang Yu Zhang Chunyu Liu Chunyu Liu Lanming Chen Yong Lin Lu Xie Lu Xie Lu Xie |
| author_sort | Manman Lu |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-04-13T09:41:50Z |
| format | Article |
| id | doaj.art-4a40ee39a88d409cb4e41496a57250ae |
| institution | Directory Open Access Journal |
| issn | 1664-3224 |
| language | English |
| last_indexed | 2024-04-13T09:41:50Z |
| publishDate | 2022-04-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Immunology |
| spelling | doaj.art-4a40ee39a88d409cb4e41496a57250ae2022-12-22T02:51:53ZengFrontiers Media S.A.Frontiers in Immunology1664-32242022-04-011310.3389/fimmu.2022.855976855976dbPepNeo2.0: A Database for Human Tumor Neoantigen Peptides From Mass Spectrometry and TCR RecognitionManman Lu0Manman Lu1Linfeng Xu2Linfeng Xu3Xingxing Jian4Xingxing Jian5Xiaoxiu Tan6Xiaoxiu Tan7Jingjing Zhao8Jingjing Zhao9Zhenhao Liu10Yu Zhang11Yu Zhang12Chunyu Liu13Chunyu Liu14Lanming Chen15Yong Lin16Lu Xie17Lu Xie18Lu Xie19College of Food Science and Technology, Shanghai Ocean University, Shanghai, ChinaShanghai-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, ChinaShanghai-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, ChinaSchool of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, ChinaShanghai-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, ChinaBioinformatics Center, National Clinical Research Centre for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, ChinaShanghai-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, ChinaDepartment of Bioinformatics and Biostatistics, Shanghai Jiao Tong University, Shanghai, ChinaCollege of Food Science and Technology, Shanghai Ocean University, Shanghai, ChinaShanghai-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, ChinaShanghai-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, ChinaShanghai-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, ChinaSchool of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, ChinaCollege of Food Science and Technology, Shanghai Ocean University, Shanghai, ChinaShanghai-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, ChinaCollege of Food Science and Technology, Shanghai Ocean University, Shanghai, ChinaSchool of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, ChinaCollege of Food Science and Technology, Shanghai Ocean University, Shanghai, ChinaShanghai-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, ChinaBioinformatics Center, National Clinical Research Centre for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, ChinaNeoantigens 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.https://www.frontiersin.org/articles/10.3389/fimmu.2022.855976/fullneoantigenmass spectrometryexperimental validationTCRdeep learning |
| spellingShingle | Manman Lu Manman Lu Linfeng Xu Linfeng Xu Xingxing Jian Xingxing Jian Xiaoxiu Tan Xiaoxiu Tan Jingjing Zhao Jingjing Zhao Zhenhao Liu Yu Zhang Yu Zhang Chunyu Liu Chunyu Liu Lanming Chen Yong Lin Lu Xie Lu Xie Lu Xie dbPepNeo2.0: A Database for Human Tumor Neoantigen Peptides From Mass Spectrometry and TCR Recognition Frontiers in Immunology neoantigen mass spectrometry experimental validation TCR deep learning |
| title | dbPepNeo2.0: A Database for Human Tumor Neoantigen Peptides From Mass Spectrometry and TCR Recognition |
| title_full | dbPepNeo2.0: A Database for Human Tumor Neoantigen Peptides From Mass Spectrometry and TCR Recognition |
| title_fullStr | dbPepNeo2.0: A Database for Human Tumor Neoantigen Peptides From Mass Spectrometry and TCR Recognition |
| title_full_unstemmed | dbPepNeo2.0: A Database for Human Tumor Neoantigen Peptides From Mass Spectrometry and TCR Recognition |
| title_short | dbPepNeo2.0: A Database for Human Tumor Neoantigen Peptides From Mass Spectrometry and TCR Recognition |
| title_sort | dbpepneo2 0 a database for human tumor neoantigen peptides from mass spectrometry and tcr recognition |
| topic | neoantigen mass spectrometry experimental validation TCR deep learning |
| url | https://www.frontiersin.org/articles/10.3389/fimmu.2022.855976/full |
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