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Journal of Integrative Bioinformatics

Editor-in-Chief: Schreiber, Falk / Hofestädt, Ralf

Managing Editor: Sommer, Björn

Ed. by Baumbach, Jan / Chen, Ming / Orlov, Yuriy / Allmer, Jens

Editorial Board: Giorgetti, Alejandro / Harrison, Andrew / Kochetov, Aleksey / Krüger, Jens / Ma, Qi / Matsuno, Hiroshi / Mitra, Chanchal K. / Pauling, Josch K. / Rawlings, Chris / Fdez-Riverola, Florentino / Romano, Paolo / Röttger, Richard / Shoshi, Alban / Soares, Siomar de Castro / Taubert, Jan / Tauch, Andreas / Yousef, Malik / Weise, Stephan / Hassani-Pak, Keywan


CiteScore 2017: 0.77

SCImago Journal Rank (SJR) 2017: 0.336

Open Access
Online
ISSN
1613-4516
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Volume 9, Issue 2

Issues

Knowledge Enrichment Analysis for Human Tissue- Specific Genes Uncover New Biological Insights

Xiu-Jun Gong
  • Corresponding author
  • School of Computer Science and Technology, Tianjin University, Weijin Rd No. 92, Nankan, Tianjin, 300072, China
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/ Hua Yu
  • School of Computer Science and Technology, Tianjin University, Weijin Rd No. 92, Nankan, Tianjin, 300072, China
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/ Chun-Bai Yang
  • School of Computer Science and Technology, Tianjin University, Weijin Rd No. 92, Nankan, Tianjin, 300072, China
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  • De Gruyter OnlineGoogle Scholar
/ Yuan-Fang Li
  • Clayton School of IT, Faculty of Information Technology,Monash University, Wellington Rd, Clayton, Vic 3800, Australia
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Published Online: 2016-10-18 | DOI: https://doi.org/10.1515/jib-2012-194

Summary

The expression and regulation of genes in different tissues are fundamental questions to be answered in biology. Knowledge enrichment analysis for tissue specific (TS) and housekeeping (HK) genes may help identify their roles in biological process or diseases and gain new biological insights.In this paper, we performed the knowledge enrichment analysis for 17,343 genes in 84 human tissues using Gene Set Enrichment Analysis (GSEA) and Hypergeometric Analysis (HA) against three biological ontologies: Gene Ontology (GO), KEGG pathways and Disease Ontology (DO) respectively.The analyses results demonstrated that the functions of most gene groups are consistent with their tissue origins. Meanwhile three interesting new associations for HK genes and the skeletal muscle tissuegenes are found. Firstly, Hypergeometric analysis against KEGG database for HK genes disclosed that three disease terms (Parkinson’s disease, Huntington’s disease, Alzheimer’s disease) are intensively enriched.Secondly, Hypergeometric analysis against the KEGG database for Skeletal Muscle tissue genes shows that two cardiac diseases of “Hypertrophic cardiomyopathy (HCM)” and “Arrhythmogenic right ventricular cardiomyopathy (ARVC)” are heavily enriched, which are also considered as no relationship with skeletal functions.Thirdly, “Prostate cancer” is intensively enriched in Hypergeometric analysis against the disease ontology (DO) for the Skeletal Muscle tissue genes, which is a much unexpected phenomenon.

About the article

Published Online: 2016-10-18

Published in Print: 2012-06-01


Citation Information: Journal of Integrative Bioinformatics, Volume 9, Issue 2, Pages 28–39, ISSN (Online) 1613-4516, DOI: https://doi.org/10.1515/jib-2012-194.

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© 2012 The Author(s). Published by Journal of Integrative Bioinformatics.. This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 License. BY-NC-ND 4.0

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