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. 2019 Jun 1;35(11):1966-1967.
doi: 10.1093/bioinformatics/bty890.

TissueEnrich: Tissue-specific gene enrichment analysis

Ashish Jain  1   2 , Geetu Tuteja  1   2
Affiliations

TissueEnrich: Tissue-specific gene enrichment analysis

Ashish Jain et al. Bioinformatics. .

Abstract

Summary: 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.

Availability and implementation: 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 information: Supplementary data are available at Bioinformatics online.

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References

    1. Ardlie K.G., et al. (2015) The genotype-tissue expression (GTEx) pilot analysis: multitissue gene regulation in humans. Science, 348, 648–660. - PMC - PubMed
    1. Jain A., et al. (2017) Deciphering transcriptional regulation in human embryonic stem cells specified towards a trophoblast fate. Sci. Rep., 7, 17257. - PMC - PubMed
    1. Komljenovic A., et al. (2016) BgeeDB, an R package for retrieval of curated expression datasets and for gene list expression localization enrichment tests. F1000Research, 5, 2748. - PMC - PubMed
    1. Petryszak R., et al. (2016) Expression atlas update—an integrated database of gene and protein expression in humans, animals and plants. Nucleic Acids Res., 44, D746–D752. - PMC - PubMed
    1. Roberts R.M., et al. (2014) Differentiation of trophoblast cells from human embryonic stem cells: to be or not to be? Reproduction, 147, D1–D12. - PubMed

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