TANTIGEN 2.0: An online database and analysis platform for tumor T cell antigens

Guanglan Zhang; Lou Chitkushev; Derin B. Keskin; Vladimir Brusic

doi:10.1109/BIBM47256.2019.8983392

TANTIGEN 2.0: An online database and analysis platform for tumor T cell antigens

Guanglan Zhang
, Lou Chitkushev
, Derin B. Keskin
, Vladimir Brusic

School of Economics

Research output: Chapter in Book/Conference proceeding › Conference contribution › peer-review

4 Citations (Scopus)

Abstract

We previously developed TANTIGEN, a comprehensive web-based database cataloging more than 1,000 T cell epitopes and HLA ligands from 292 tumor antigens. TANTIGEN 2.0 is significantly expanded the number and coverage of immune response targets (T cell epitopes and HLA ligands) of previously cataloged tumor antigens. We expanded the number of cataloged tumor antigens to more than 4,000 and have added their reported targets of immune responses. We also included neoantigens, a new class of tumor antigens generated through mutations that results in a new amino acid sequence in tumor antigens. TANTIGEN 2.0 contains validated TCR sequences specific for cognate T cell epitopes. Gene expression information was extracted from tumor antigen gene/mRNA/protein expression information in major human cancers provided by Human Pathology Atlas. TANTIGEN 2.0 provides a rich data resource for tumor-associated epitope and neoepitope discovery studies. It is freely available at http://projects.met-hilab.org/tadb.

Original language	English
Title of host publication	Proceedings - 2019 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2019
Editors	Illhoi Yoo, Jinbo Bi, Xiaohua Tony Hu
Publisher	Institute of Electrical and Electronics Engineers Inc.
Pages	2228-2231
Number of pages	4
ISBN (Electronic)	9781728118673
DOIs	https://doi.org/10.1109/BIBM47256.2019.8983392
Publication status	Published - Nov 2019
Event	2019 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2019 - San Diego, United States Duration: 18 Nov 2019 → 21 Nov 2019

Publication series

Name	Proceedings - 2019 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2019

Conference

Conference	2019 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2019
Country/Territory	United States
City	San Diego
Period	18/11/19 → 21/11/19

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

SDG 3 Good Health and Well-being

Free Keywords

T cell epitope prediction
cancer vaccine
immunotherapy
neoantigen
neoepitope
tumor antigen

ASJC Scopus subject areas

Biochemistry
Biotechnology
Molecular Medicine
Modelling and Simulation
Health Informatics
Pharmacology (medical)
Public Health, Environmental and Occupational Health

Access to Document

10.1109/BIBM47256.2019.8983392

Cite this

Zhang, G., Chitkushev, L., Keskin, D. B., & Brusic, V. (2019). TANTIGEN 2.0: An online database and analysis platform for tumor T cell antigens. In I. Yoo, J. Bi, & X. T. Hu (Eds.), Proceedings - 2019 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2019 (pp. 2228-2231). Article 8983392 (Proceedings - 2019 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2019). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/BIBM47256.2019.8983392

Zhang, Guanglan ; Chitkushev, Lou ; Keskin, Derin B. et al. / TANTIGEN 2.0 : An online database and analysis platform for tumor T cell antigens. Proceedings - 2019 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2019. editor / Illhoi Yoo ; Jinbo Bi ; Xiaohua Tony Hu. Institute of Electrical and Electronics Engineers Inc., 2019. pp. 2228-2231 (Proceedings - 2019 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2019).

@inproceedings{e826a2b9ce644d8c9d58273885401a25,

title = "TANTIGEN 2.0: An online database and analysis platform for tumor T cell antigens",

abstract = "We previously developed TANTIGEN, a comprehensive web-based database cataloging more than 1,000 T cell epitopes and HLA ligands from 292 tumor antigens. TANTIGEN 2.0 is significantly expanded the number and coverage of immune response targets (T cell epitopes and HLA ligands) of previously cataloged tumor antigens. We expanded the number of cataloged tumor antigens to more than 4,000 and have added their reported targets of immune responses. We also included neoantigens, a new class of tumor antigens generated through mutations that results in a new amino acid sequence in tumor antigens. TANTIGEN 2.0 contains validated TCR sequences specific for cognate T cell epitopes. Gene expression information was extracted from tumor antigen gene/mRNA/protein expression information in major human cancers provided by Human Pathology Atlas. TANTIGEN 2.0 provides a rich data resource for tumor-associated epitope and neoepitope discovery studies. It is freely available at http://projects.met-hilab.org/tadb.",

keywords = "T cell epitope prediction, cancer vaccine, immunotherapy, neoantigen, neoepitope, tumor antigen",

author = "Guanglan Zhang and Lou Chitkushev and Keskin, \{Derin B.\} and Vladimir Brusic",

note = "Publisher Copyright: {\textcopyright} 2019 IEEE.; 2019 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2019 ; Conference date: 18-11-2019 Through 21-11-2019",

year = "2019",

month = nov,

doi = "10.1109/BIBM47256.2019.8983392",

language = "English",

series = "Proceedings - 2019 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2019",

publisher = "Institute of Electrical and Electronics Engineers Inc.",

pages = "2228--2231",

editor = "Illhoi Yoo and Jinbo Bi and Hu, \{Xiaohua Tony\}",

booktitle = "Proceedings - 2019 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2019",

address = "United States",

}

Zhang, G, Chitkushev, L, Keskin, DB & Brusic, V 2019, TANTIGEN 2.0: An online database and analysis platform for tumor T cell antigens. in I Yoo, J Bi & XT Hu (eds), Proceedings - 2019 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2019., 8983392, Proceedings - 2019 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2019, Institute of Electrical and Electronics Engineers Inc., pp. 2228-2231, 2019 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2019, San Diego, United States, 18/11/19. https://doi.org/10.1109/BIBM47256.2019.8983392

TANTIGEN 2.0: An online database and analysis platform for tumor T cell antigens. / Zhang, Guanglan; Chitkushev, Lou; Keskin, Derin B. et al.
Proceedings - 2019 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2019. ed. / Illhoi Yoo; Jinbo Bi; Xiaohua Tony Hu. Institute of Electrical and Electronics Engineers Inc., 2019. p. 2228-2231 8983392 (Proceedings - 2019 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2019).

Research output: Chapter in Book/Conference proceeding › Conference contribution › peer-review

TY - GEN

T1 - TANTIGEN 2.0

T2 - 2019 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2019

AU - Zhang, Guanglan

AU - Chitkushev, Lou

AU - Keskin, Derin B.

AU - Brusic, Vladimir

PY - 2019/11

Y1 - 2019/11

N2 - We previously developed TANTIGEN, a comprehensive web-based database cataloging more than 1,000 T cell epitopes and HLA ligands from 292 tumor antigens. TANTIGEN 2.0 is significantly expanded the number and coverage of immune response targets (T cell epitopes and HLA ligands) of previously cataloged tumor antigens. We expanded the number of cataloged tumor antigens to more than 4,000 and have added their reported targets of immune responses. We also included neoantigens, a new class of tumor antigens generated through mutations that results in a new amino acid sequence in tumor antigens. TANTIGEN 2.0 contains validated TCR sequences specific for cognate T cell epitopes. Gene expression information was extracted from tumor antigen gene/mRNA/protein expression information in major human cancers provided by Human Pathology Atlas. TANTIGEN 2.0 provides a rich data resource for tumor-associated epitope and neoepitope discovery studies. It is freely available at http://projects.met-hilab.org/tadb.

AB - We previously developed TANTIGEN, a comprehensive web-based database cataloging more than 1,000 T cell epitopes and HLA ligands from 292 tumor antigens. TANTIGEN 2.0 is significantly expanded the number and coverage of immune response targets (T cell epitopes and HLA ligands) of previously cataloged tumor antigens. We expanded the number of cataloged tumor antigens to more than 4,000 and have added their reported targets of immune responses. We also included neoantigens, a new class of tumor antigens generated through mutations that results in a new amino acid sequence in tumor antigens. TANTIGEN 2.0 contains validated TCR sequences specific for cognate T cell epitopes. Gene expression information was extracted from tumor antigen gene/mRNA/protein expression information in major human cancers provided by Human Pathology Atlas. TANTIGEN 2.0 provides a rich data resource for tumor-associated epitope and neoepitope discovery studies. It is freely available at http://projects.met-hilab.org/tadb.

KW - T cell epitope prediction

KW - cancer vaccine

KW - immunotherapy

KW - neoantigen

KW - neoepitope

KW - tumor antigen

UR - https://www.scopus.com/pages/publications/85083894030

U2 - 10.1109/BIBM47256.2019.8983392

DO - 10.1109/BIBM47256.2019.8983392

M3 - Conference contribution

AN - SCOPUS:85083894030

T3 - Proceedings - 2019 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2019

SP - 2228

EP - 2231

BT - Proceedings - 2019 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2019

A2 - Yoo, Illhoi

A2 - Bi, Jinbo

A2 - Hu, Xiaohua Tony

PB - Institute of Electrical and Electronics Engineers Inc.

Y2 - 18 November 2019 through 21 November 2019

ER -

Zhang G, Chitkushev L, Keskin DB, Brusic V. TANTIGEN 2.0: An online database and analysis platform for tumor T cell antigens. In Yoo I, Bi J, Hu XT, editors, Proceedings - 2019 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2019. Institute of Electrical and Electronics Engineers Inc. 2019. p. 2228-2231. 8983392. (Proceedings - 2019 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2019). doi: 10.1109/BIBM47256.2019.8983392

TANTIGEN 2.0: An online database and analysis platform for tumor T cell antigens

Abstract

Publication series

Conference

UN SDGs

Free Keywords

ASJC Scopus subject areas

Access to Document

Other files and links

Fingerprint

Cite this