TSGOE: A web tool for tissue-specific gene ontology enrichment

Jiajie Peng; Guilin Lu; Hansheng Xue; Tao Wang; Xuequn Shang

doi:10.1109/BIBM.2018.8621204

TSGOE: A web tool for tissue-specific gene ontology enrichment

Jiajie Peng, Guilin Lu, Hansheng Xue, Tao Wang, Xuequn Shang

School of Computer Science

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

Abstract

Gene Ontology (GO) is one of the most popular Bioinformatics resources for studying the functional relationships between genes. GO enrichment analysis has become a routine method for gene function analysis, and it is of great significance for revealing the molecular mechanism of biology. However, existing GO enrichment analysis tools do not take into account tissue specificity and cannot distinguish gene sets that users interested. In this paper, we propose an easy-to-use web application, termed as TSGOE, which allows users to perform tissue specific-based GO enrichment analysis conveniently. Besides, TSGOE also provides rigorous statistical testing to improve the reliability of analytical result. To evaluate its performance, we apply TSGOE on several cancer-related gene lists. The experimental results show that our tool perform better than traditional GO enrichment analysis method. TSGOE is available at http://120.77.47.2:5678.

Original language	English
Title of host publication	Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018
Editors	Harald Schmidt, David Griol, Haiying Wang, Jan Baumbach, Huiru Zheng, Zoraida Callejas, Xiaohua Hu, Julie Dickerson, Le Zhang
Publisher	Institute of Electrical and Electronics Engineers Inc.
Pages	1266-1269
Number of pages	4
ISBN (Electronic)	9781538654880
DOIs	https://doi.org/10.1109/BIBM.2018.8621204
State	Published - 21 Jan 2019
Event	2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018 - Madrid, Spain Duration: 3 Dec 2018 → 6 Dec 2018

Publication series

Name	Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018

Conference

Conference	2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018
Country/Territory	Spain
City	Madrid
Period	3/12/18 → 6/12/18

Keywords

enrichment analysis
Gene Ontology
tissue-specific
web tool

UN SDGs

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

Access to Document

10.1109/BIBM.2018.8621204

Cite this

Peng, J., Lu, G., Xue, H., Wang, T., & Shang, X. (2019). TSGOE: A web tool for tissue-specific gene ontology enrichment. In H. Schmidt, D. Griol, H. Wang, J. Baumbach, H. Zheng, Z. Callejas, X. Hu, J. Dickerson, & L. Zhang (Eds.), Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018 (pp. 1266-1269). Article 8621204 (Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/BIBM.2018.8621204

Peng, Jiajie ; Lu, Guilin ; Xue, Hansheng et al. / TSGOE : A web tool for tissue-specific gene ontology enrichment. Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018. editor / Harald Schmidt ; David Griol ; Haiying Wang ; Jan Baumbach ; Huiru Zheng ; Zoraida Callejas ; Xiaohua Hu ; Julie Dickerson ; Le Zhang. Institute of Electrical and Electronics Engineers Inc., 2019. pp. 1266-1269 (Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018).

@inproceedings{08ee9ba09e5e4ba4812c7e385bf1f90a,

title = "TSGOE: A web tool for tissue-specific gene ontology enrichment",

abstract = "Gene Ontology (GO) is one of the most popular Bioinformatics resources for studying the functional relationships between genes. GO enrichment analysis has become a routine method for gene function analysis, and it is of great significance for revealing the molecular mechanism of biology. However, existing GO enrichment analysis tools do not take into account tissue specificity and cannot distinguish gene sets that users interested. In this paper, we propose an easy-to-use web application, termed as TSGOE, which allows users to perform tissue specific-based GO enrichment analysis conveniently. Besides, TSGOE also provides rigorous statistical testing to improve the reliability of analytical result. To evaluate its performance, we apply TSGOE on several cancer-related gene lists. The experimental results show that our tool perform better than traditional GO enrichment analysis method. TSGOE is available at http://120.77.47.2:5678.",

keywords = "enrichment analysis, Gene Ontology, tissue-specific, web tool",

author = "Jiajie Peng and Guilin Lu and Hansheng Xue and Tao Wang and Xuequn Shang",

note = "Publisher Copyright: {\textcopyright} 2018 IEEE.; 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018 ; Conference date: 03-12-2018 Through 06-12-2018",

year = "2019",

month = jan,

day = "21",

doi = "10.1109/BIBM.2018.8621204",

language = "英语",

series = "Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018",

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

pages = "1266--1269",

editor = "Harald Schmidt and David Griol and Haiying Wang and Jan Baumbach and Huiru Zheng and Zoraida Callejas and Xiaohua Hu and Julie Dickerson and Le Zhang",

booktitle = "Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018",

}

Peng, J, Lu, G, Xue, H, Wang, T & Shang, X 2019, TSGOE: A web tool for tissue-specific gene ontology enrichment. in H Schmidt, D Griol, H Wang, J Baumbach, H Zheng, Z Callejas, X Hu, J Dickerson & L Zhang (eds), Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018., 8621204, Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018, Institute of Electrical and Electronics Engineers Inc., pp. 1266-1269, 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018, Madrid, Spain, 3/12/18. https://doi.org/10.1109/BIBM.2018.8621204

TSGOE: A web tool for tissue-specific gene ontology enrichment. / Peng, Jiajie; Lu, Guilin; Xue, Hansheng et al.
Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018. ed. / Harald Schmidt; David Griol; Haiying Wang; Jan Baumbach; Huiru Zheng; Zoraida Callejas; Xiaohua Hu; Julie Dickerson; Le Zhang. Institute of Electrical and Electronics Engineers Inc., 2019. p. 1266-1269 8621204 (Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018).

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

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T1 - TSGOE

T2 - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018

AU - Peng, Jiajie

AU - Lu, Guilin

AU - Xue, Hansheng

AU - Wang, Tao

AU - Shang, Xuequn

PY - 2019/1/21

Y1 - 2019/1/21

N2 - Gene Ontology (GO) is one of the most popular Bioinformatics resources for studying the functional relationships between genes. GO enrichment analysis has become a routine method for gene function analysis, and it is of great significance for revealing the molecular mechanism of biology. However, existing GO enrichment analysis tools do not take into account tissue specificity and cannot distinguish gene sets that users interested. In this paper, we propose an easy-to-use web application, termed as TSGOE, which allows users to perform tissue specific-based GO enrichment analysis conveniently. Besides, TSGOE also provides rigorous statistical testing to improve the reliability of analytical result. To evaluate its performance, we apply TSGOE on several cancer-related gene lists. The experimental results show that our tool perform better than traditional GO enrichment analysis method. TSGOE is available at http://120.77.47.2:5678.

AB - Gene Ontology (GO) is one of the most popular Bioinformatics resources for studying the functional relationships between genes. GO enrichment analysis has become a routine method for gene function analysis, and it is of great significance for revealing the molecular mechanism of biology. However, existing GO enrichment analysis tools do not take into account tissue specificity and cannot distinguish gene sets that users interested. In this paper, we propose an easy-to-use web application, termed as TSGOE, which allows users to perform tissue specific-based GO enrichment analysis conveniently. Besides, TSGOE also provides rigorous statistical testing to improve the reliability of analytical result. To evaluate its performance, we apply TSGOE on several cancer-related gene lists. The experimental results show that our tool perform better than traditional GO enrichment analysis method. TSGOE is available at http://120.77.47.2:5678.

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KW - tissue-specific

KW - web tool

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M3 - 会议稿件

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T3 - Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018

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BT - Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018

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A2 - Griol, David

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A2 - Baumbach, Jan

A2 - Zheng, Huiru

A2 - Callejas, Zoraida

A2 - Hu, Xiaohua

A2 - Dickerson, Julie

A2 - Zhang, Le

PB - Institute of Electrical and Electronics Engineers Inc.

Y2 - 3 December 2018 through 6 December 2018

ER -

Peng J, Lu G, Xue H, Wang T, Shang X. TSGOE: A web tool for tissue-specific gene ontology enrichment. In Schmidt H, Griol D, Wang H, Baumbach J, Zheng H, Callejas Z, Hu X, Dickerson J, Zhang L, editors, Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018. Institute of Electrical and Electronics Engineers Inc. 2019. p. 1266-1269. 8621204. (Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018). doi: 10.1109/BIBM.2018.8621204

TSGOE: A web tool for tissue-specific gene ontology enrichment

Abstract

Publication series

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Keywords

UN SDGs

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