{"id":11,"date":"2019-06-24T02:21:49","date_gmt":"2019-06-24T02:21:49","guid":{"rendered":"https:\/\/pgx.zju.edu.cn\/tsnad\/?page_id=11"},"modified":"2021-09-02T11:42:25","modified_gmt":"2021-09-02T11:42:25","slug":"help","status":"publish","type":"page","link":"https:\/\/pgx.zju.edu.cn\/tsnad\/help\/","title":{"rendered":"help"},"content":{"rendered":"\n

Browser compatibility<\/strong><\/p>\n\n\n\n
OS<\/td>Version<\/td>Chrome<\/td>Firefox<\/td><\/tr>
Linux<\/td>Ubuntu 18.04 <\/td>78.0<\/td>70.0.1<\/td><\/tr>
Windows<\/td>10<\/td> 78.0 <\/td>70.0.1<\/td><\/tr><\/tbody><\/table>\n\n\n\n

1.The detailed example<\/strong><\/h4>\n\n\n\n

vcf<\/strong> file: mutect_call.vcf<\/a> The vcf file should be obtained from either MuTect or MuTect2. <\/p>\n\n\n\n

2. The meaning of each parameter<\/strong> in the results<\/h4>\n\n\n\n
Annotation<\/th>HLA<\/th>Peptide<\/th>Binding score<\/th>Immunogenic score<\/th>Rank<\/th><\/tr><\/thead>
RYR2_V1476L_8<\/td>HLA-A01:03<\/td>LGDEKGKLHE<\/td>0.9684<\/td>0.545<\/td>0<\/td><\/tr>
RYR2_V1476L_8<\/td>HLA-A01:03<\/td>LGDEKGKLHES<\/td>0.9987<\/td>0.5566<\/td>0<\/td><\/tr>
SLC9B1_I279M_6<\/td>HLA-A01:03<\/td>FSSGGMLN<\/td>0.9883<\/td>0.5324<\/td>0<\/td><\/tr>
SLC9B1_I279M_6<\/td>HLA-A01:03<\/td>FSSGGMLNN<\/td>0.4751<\/td>0.5275<\/td>0<\/td><\/tr>
POMGNT2_L526M_5<\/td>HLA-A01:03<\/td>YEVWMQEQ<\/td>0.9516<\/td>0.5423<\/td>1<\/td><\/tr>
SLC9B1_I279M_6<\/td>HLA-A01:03<\/td>FSSGGMLNNA<\/td>0.8862<\/td>0.5214<\/td>1<\/td><\/tr>
SLC9B1_I279M_7<\/td>HLA-A01:03<\/td>VFSSGGMLN<\/td>0.0034<\/td>0.5061<\/td>1<\/td><\/tr>
TMCC1_AA180-181A_3<\/td>HLA-A01:03<\/td>AAACLPGEEGT<\/td>0.9607<\/td>0.5417<\/td>1<\/td><\/tr>
SLC9B1_I279M_7<\/td>HLA-A01:03<\/td>VFSSGGMLNN<\/td>0.6364<\/td>0.5065<\/td>2<\/td><\/tr>
SYT3_P544L_4<\/td>HLA-A01:03<\/td>AADLHGREHWA<\/td>0.8917<\/td>0.5011<\/td>2<\/td><\/tr><\/tbody><\/table>\n\n\n\n

In the predicted result, all the HLA-peptide pairs with immunogenicity score less than 0.5 was discarded and not shown in the result table. <\/p>\n\n\n\n

Annotation<\/strong>: normally, the content in this column includes gene name<\/em>, mutation position in protein<\/em> and the position of mutated amino acid in peptide.<\/em><\/p>\n\n\n\n

Binding score<\/strong>: the score predicted by binding model of DeepHLApan.<\/p>\n\n\n\n

Immunogenicity score<\/strong> : the score predicted by immunogenicity model of DeepHLApan. 0.5 is the threshold to select the predicted immunogenic pHLA.<\/p>\n\n\n\n

Rank<\/strong> : the HLA-peptide pairs were ranked according to their predicted binding score across different length of peptide.<\/p>\n\n\n\n

3.Contact<\/strong><\/h4>\n\n\n\n

E-mail:<\/strong>        zhanzhou@zju.edu.cn<\/a><\/p>\n\n\n\n

Address: <\/strong>     College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang<\/p>\n\n\n\n

Citation:<\/strong> <\/p>\n\n\n\n

1. Zhou Z#<\/sup>,\u00a0<\/strong>Lyu X#<\/sup>,\u00a0Wu 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<\/strong>.\u00a0R Soc Open Sci. 2017, 4: 170050. https:\/\/doi.org\/10.1098\/rsos.170050 <\/a><\/p>\n\n\n\n

2. Wu J, Wang W, Zhang J, Zhou B, Zhao W, Su Z, Gu X, Wu J,\u00a0Zhou Z*<\/sup><\/strong>, Chen S*<\/sup>.\u00a0DeepHLApan: A deep learning approach for neoantigen prediction considering both HLA-peptide binding and immunogenicity.<\/strong>\u00a0Front Immunol, 2019, 10: 2559. https:\/\/doi.org\/10.3389\/fimmu.2019.02559<\/a> <\/p>\n\n\n\n

3. Zhou Z#,<\/sup>*,\u00a0Wu J#<\/sup>, Ren J, Chen W, Zhao W, Gu X, Chi Y, He Q, Yang B, Wu J*, Chen S*. TSNAD v2.0: A one-stop software solution for tumor-specific neoantigen detection<\/strong>. Comput Struct Biotechnol J, 2021, 19:4510-4516. https:\/\/doi.org\/10.1016\/j.csbj.2021.08.016<\/a><\/p>\n\n\n\n

<\/p>\n","protected":false},"excerpt":{"rendered":"

Browser compatibility OS Version Chrome Firefox Linux Ubuntu 18.04 78.0 70.0.1 Windows 10 78.0 70.0.1 1.The detailed example vcf file:…<\/p>\n","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"home.php","meta":{"footnotes":""},"class_list":["post-11","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/pgx.zju.edu.cn\/tsnad\/wp-json\/wp\/v2\/pages\/11"}],"collection":[{"href":"https:\/\/pgx.zju.edu.cn\/tsnad\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/pgx.zju.edu.cn\/tsnad\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/pgx.zju.edu.cn\/tsnad\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/pgx.zju.edu.cn\/tsnad\/wp-json\/wp\/v2\/comments?post=11"}],"version-history":[{"count":14,"href":"https:\/\/pgx.zju.edu.cn\/tsnad\/wp-json\/wp\/v2\/pages\/11\/revisions"}],"predecessor-version":[{"id":227,"href":"https:\/\/pgx.zju.edu.cn\/tsnad\/wp-json\/wp\/v2\/pages\/11\/revisions\/227"}],"wp:attachment":[{"href":"https:\/\/pgx.zju.edu.cn\/tsnad\/wp-json\/wp\/v2\/media?parent=11"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}