TissueEnrich: Tissue-specific gene enrichment analysis

Bioinformatics
Ashish Jain, Geetu Tuteja

Abstract

RNA-Seq data analysis results in lists of genes that may have a similar function, based on differential gene expression analysis or co-expression network analysis. While tools have been developed to identify biological processes that are enriched in the genes sets, there remains a need for tools that identify enrichment of tissue-specific genes. Therefore, we developed TissueEnrich, a tool that calculates tissue-specific gene enrichment in an input gene set. We demonstrated that TissueEnrich can assign tissue identities to single cell clusters and differentiated embryonic stem cells. The TissueEnrich web application is freely available at http://tissueenrich.gdcb.iastate.edu/. The R package is available through Bioconductor at https://bioconductor.org/packages/TissueEnrich. Both the web application and R package are for non-profit academic use under the MIT license. Supplementary data are available at Bioinformatics online.

References

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Citations

Jan 7, 2004·Genome Research·Eitan E WinterChris P Ponting
Jan 24, 2014·The Journal of Neuroscience : the Official Journal of the Society for Neuroscience·Xiaoxiao XuJoseph D Dougherty
Feb 13, 2014·Reproduction : the Official Journal of the Society for the Study of Fertility·R Michael RobertsRoger A Pedersen
Jan 24, 2015·Science·Mathias UhlénFredrik Pontén
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Nov 21, 2017·Nucleic Acids Research·Daniel R ZerbinoPaul Flicek
Dec 1, 2017·Nature Communications·Kyoko WatanabeDanielle Posthuma

Related Concepts

Laboratory Procedures
Genes
Bio-Informatics
Gene Expression
Cell Differentiation Process
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Human Embryonic Stem Cells
Analysis
Embryonic Stem Cells
RNA Analysis

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