{"id":15,"date":"2018-01-02T05:09:21","date_gmt":"2018-01-02T05:09:21","guid":{"rendered":"https:\/\/pgx.zju.edu.cn\/wordpress\/?page_id=15"},"modified":"2022-04-02T11:37:21","modified_gmt":"2022-04-02T11:37:21","slug":"about","status":"publish","type":"page","link":"https:\/\/pgx.zju.edu.cn\/tsnadb1\/about\/","title":{"rendered":"About"},"content":{"rendered":"
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Citations<\/h3>\n
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Please cite us if you find this resource useful:<\/p>\n

[1]. Wu J, Zhao W, Zhou B, Su Z, Gu X,\u00a0Zhou Z*, Chen S*. TSNAdb: a database for tumor-specific neoantigens from immunogenomics data analysis.\u00a0Genomics\u00a0 Proteomics Bioinformatics. 2018, 16(4),276\u2013282. DOI: 10.1016\/j.gpb.2018.06.003<\/a>\u00a0 \"pdf<\/a><\/p>\n

[2]. Zhou Z#,\u00a0Lyu X#, Wu J, Yang X, Wu S, Zhou J, Gu X, Su Z*, Chen S*. TSNAD: an integrated software for cancer somatic mutation and tumour-specific neoantigen detection.\u00a0R Soc Open Sci. 2017, 4: 170050. DOI: 10.1098\/rsos.170050<\/a>\u00a0 \u00a0\"pdf<\/a><\/p>\n<\/div>\n<\/div>\n<\/div>\n

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Data source<\/h3>\n
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The somatic mutation data is extracted from The Cancer Genome Atlas(TCGA)<\/a> and International Cancer Genome Consortium (ICGC)<\/a>;<\/p>\n

The HLA allele information is extracted from The Cancer Immunome Atlas(TCIA)<\/a><\/p>\n

The peptide-HLA binding validation data is extracted from The Immune Epitope Database(IEDB)<\/a><\/p>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n

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Prediction methods<\/h3>\n
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\u00a0 \u00a0 \u00a0 \u00a0 \u00a0 The binding affinities\u00a0<\/b>between peptides and HLA alleles\u00a0<\/b>are predicted by NetMHCpan 2.8<\/a>\/NetMHCpan 4.0<\/a>.<\/p>\n

The\u00a0extensive analyses of potential neoantigens generated by somatic mutations of each gene are conducted by the tools embedded in TSNAD<\/a>.<\/p>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n

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Data availability<\/h3>\n
Users can download data from the\u00a0Download<\/a>\u00a0page. Data is freely available for academic users who agree with the\u00a0TCGA publication guidelines\u00a0<\/a>.<\/div>\n<\/div>\n<\/div>\n<\/div>\n
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Search guide<\/h3>\n
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Since the results are predicted by two different versions of NetMHCpan (v2.8 and v4.0), users need to select\u00a0 the preferred one (default: NetMHCpan 2.8). Then, users can input the\u00a0gene name (e.g. KRAS<\/em>)<\/b>\u00a0\u00a0to search the corresponding neoantigen results. The results will return in a few seconds.<\/p>\n

In the ‘Browse<\/strong>‘ page, the gene name is required and the tissue name is optional in each retrieval.<\/span><\/p>\n

In the result table, the description of each column is listed as follows:<\/p>\n

\u00a0 \u00a0 \u00a0 \u00a0 \u00a0Tissue<\/strong>: tumor type.<\/span><\/p>\n

\u00a0 \u00a0 \u00a0 \u00a0 \u00a0Mutation<\/strong>: amino acid change caused by the mutation. Users can obtain the detailed information by clicking on the mutation.<\/span><\/p>\n

\u00a0 \u00a0 \u00a0 \u00a0 \u00a0Position in peptide<\/strong>: the mutation position in peptide (e.g. if the value is 8 and the peptide is\u00a0EVFHACINWV, the mutant amino acid residue would be N).<\/span><\/p>\n

\u00a0 \u00a0 \u00a0 \u00a0 \u00a0HLA allele<\/strong>: HLA allele.<\/span><\/p>\n

\u00a0 \u00a0 \u00a0 \u00a0 \u00a0WT peptide<\/strong>: the sequence of wild-type peptide.<\/span><\/p>\n

\u00a0 \u00a0 \u00a0 \u00a0\u00a0 WT affinity<\/strong>: the predicted binding affinity between wild-type peptide and HLA allele by NetMHCpan2.8 (4.0).\u00a0<\/span><\/p>\n

\u00a0 \u00a0 \u00a0 \u00a0\u00a0 WT binding level<\/strong>: binding level between wild-type peptide and HLA allele.\u00a0 ‘SB’ indicates strong binding (IC50 < 150nM) ,\u00a0 ‘WB’ indicates weak binding (150nM < IC50\u00a0 < 500nM),\u00a0 ‘- ‘ indicates non-binding (IC50 > 500nM).<\/span><\/p>\n

\u00a0 \u00a0 \u00a0 \u00a0 \u00a0MT peptide<\/strong>: the sequence of mutant peptide.<\/span><\/p>\n

\u00a0 \u00a0 \u00a0 \u00a0 \u00a0MT affinity<\/strong>:the predicted binding affinity between mutant peptide and HLA allele by NetMHCpan2.8 (4.0).<\/span><\/p>\n

\u00a0 \u00a0 \u00a0 \u00a0 \u00a0MT binding level<\/strong>: binding level between mutant peptide and HLA allele .<\/span><\/p>\n

\u00a0 \u00a0 \u00a0 \u00a0 \u00a0Frequency in the tissue<\/strong>: neoantigen frequency in the samples of specific tumor type.<\/span><\/p>\n

\u00a0 \u00a0 \u00a0 \u00a0 \u00a0Frequency in all<\/strong> samples<\/strong>: neoantigen frequency in all samples.<\/span><\/p>\n

In the ‘Search<\/strong>‘ page, the gene name is required.<\/span><\/p>\n

Each cell of the figure stands for a combination of mutation and HLA allele. Only the cell with color (neither gray nor white) represent a potential neoantigen.\u00a0<\/span><\/span><\/p>\n

\u00a0 \u00a0 \u00a0 \u00a0 \u00a0 The information in each colorful cell stands for mutation, HLA allele and the frequency of the neoantigen, respectively.\u00a0<\/span><\/p>\n

\u00a0 \u00a0 \u00a0 \u00a0 \u00a0 We arrange the result according to the frequencies of HLA alleles and mutations. The frequency of mutation decreased from upper to bottom, and the frequency of HLA allele decreased from right to left. So the most\u00a0promising potential neoantigens for tumor immunotherapy are listed on the left bottom corner.<\/span><\/p>\n

In the ‘Validation<\/strong>‘ page<\/span><\/p>\n

IEDB result<\/strong>: ‘Positvie’ indicates binding, ‘Negative’ indicates non-binding.<\/p>\n

IEDB assay ID<\/strong>: The id from IEDB, linked with the detailed information of the result (including reference, experiment assays).<\/p>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n

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Contact<\/h3>\n
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\u00a0 \u00a0 \u00a0 \u00a0 \u00a0E-mail: \u00a0 \u00a0 \u00a0 \u00a0zhanzhou@zju.edu.cn<\/a><\/p>\n

Address: \u00a0 \u00a0\u00a0 College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China.<\/p>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n","protected":false},"excerpt":{"rendered":"

Citations Please cite us if you find this resource useful: [1]. Wu J, Zhao W, Zhou B, Su Z, Gu X,\u00a0Zhou Z*, Chen S*. TSNAdb: a database for tumor-specific neoantigens…<\/p>\n","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"single.php","meta":{"footnotes":""},"class_list":["post-15","page","type-page","status-publish","hentry","entry","simple"],"_links":{"self":[{"href":"https:\/\/pgx.zju.edu.cn\/tsnadb1\/wp-json\/wp\/v2\/pages\/15","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/pgx.zju.edu.cn\/tsnadb1\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/pgx.zju.edu.cn\/tsnadb1\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/pgx.zju.edu.cn\/tsnadb1\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/pgx.zju.edu.cn\/tsnadb1\/wp-json\/wp\/v2\/comments?post=15"}],"version-history":[{"count":202,"href":"https:\/\/pgx.zju.edu.cn\/tsnadb1\/wp-json\/wp\/v2\/pages\/15\/revisions"}],"predecessor-version":[{"id":730,"href":"https:\/\/pgx.zju.edu.cn\/tsnadb1\/wp-json\/wp\/v2\/pages\/15\/revisions\/730"}],"wp:attachment":[{"href":"https:\/\/pgx.zju.edu.cn\/tsnadb1\/wp-json\/wp\/v2\/media?parent=15"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}