Integrated protocol for exitron and exitron-derived neoantigen identification using human RNA-seq data with ScanExitron and ScanNeo

Ting You Wang; Rendong Yang

doi:10.1016/j.xpro.2021.100788

Integrated protocol for exitron and exitron-derived neoantigen identification using human RNA-seq data with ScanExitron and ScanNeo

Ting You Wang
, Rendong Yang

The Hormel Institute

Research output: Contribution to journal › Article › peer-review

11 Scopus citations

Abstract

Exitron splicing (EIS) events in cancers can disrupt functional protein domains to cause cancer driver effects. EIS has been recognized as a new source of tumor neoantigens. Here, we describe an integrated protocol for EIS and EIS-derived neoantigen identification using RNA-seq data. The protocol constitutes a step-by-step guide from data collection to neoantigen prediction. For complete details on the use and execution of this protocol, please refer to Wang et al. (2021).

Original language	English (US)
Article number	100788
Journal	STAR Protocols
Volume	2
Issue number	3
DOIs	https://doi.org/10.1016/j.xpro.2021.100788
State	Published - Sep 17 2021

Bibliographical note

Publisher Copyright:
© 2021 The Author(s)

UN SDGs

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

SDG 3 Good Health and Well-being

Keywords

Bioinformatics
Cancer
Genetics
Genomics
Immunology
RNAseq

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10.1016/j.xpro.2021.100788

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title = "Integrated protocol for exitron and exitron-derived neoantigen identification using human RNA-seq data with ScanExitron and ScanNeo",

abstract = "Exitron splicing (EIS) events in cancers can disrupt functional protein domains to cause cancer driver effects. EIS has been recognized as a new source of tumor neoantigens. Here, we describe an integrated protocol for EIS and EIS-derived neoantigen identification using RNA-seq data. The protocol constitutes a step-by-step guide from data collection to neoantigen prediction. For complete details on the use and execution of this protocol, please refer to Wang et al. (2021).",

keywords = "Bioinformatics, Cancer, Genetics, Genomics, Immunology, RNAseq",

author = "Wang, \{Ting You\} and Rendong Yang",

note = "Publisher Copyright: {\textcopyright} 2021 The Author(s)",

year = "2021",

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day = "17",

doi = "10.1016/j.xpro.2021.100788",

language = "English (US)",

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T1 - Integrated protocol for exitron and exitron-derived neoantigen identification using human RNA-seq data with ScanExitron and ScanNeo

AU - Wang, Ting You

AU - Yang, Rendong

PY - 2021/9/17

Y1 - 2021/9/17

N2 - Exitron splicing (EIS) events in cancers can disrupt functional protein domains to cause cancer driver effects. EIS has been recognized as a new source of tumor neoantigens. Here, we describe an integrated protocol for EIS and EIS-derived neoantigen identification using RNA-seq data. The protocol constitutes a step-by-step guide from data collection to neoantigen prediction. For complete details on the use and execution of this protocol, please refer to Wang et al. (2021).

AB - Exitron splicing (EIS) events in cancers can disrupt functional protein domains to cause cancer driver effects. EIS has been recognized as a new source of tumor neoantigens. Here, we describe an integrated protocol for EIS and EIS-derived neoantigen identification using RNA-seq data. The protocol constitutes a step-by-step guide from data collection to neoantigen prediction. For complete details on the use and execution of this protocol, please refer to Wang et al. (2021).

KW - Bioinformatics

KW - Cancer

KW - Genetics

KW - Genomics

KW - Immunology

KW - RNAseq

UR - https://www.scopus.com/pages/publications/85122822083

UR - https://www.scopus.com/pages/publications/85122822083#tab=citedBy

U2 - 10.1016/j.xpro.2021.100788

DO - 10.1016/j.xpro.2021.100788

M3 - Article

C2 - 34522901

AN - SCOPUS:85122822083

SN - 2666-1667

VL - 2

JO - STAR Protocols

JF - STAR Protocols

IS - 3

M1 - 100788

ER -

Integrated protocol for exitron and exitron-derived neoantigen identification using human RNA-seq data with ScanExitron and ScanNeo

Abstract

Bibliographical note

UN SDGs

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