WocEA: The visualization of functional enrichment results in word clouds

Wanshan Ning; Shaofeng Lin; Jiaqi Zhou; Yaping Guo; Ying Zhang; Di Peng; Wankun Deng; Yu Xue

doi:10.1016/j.jgg.2018.02.008

Volume 45 Issue 7

Jul. 2018

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Article Navigation > Journal of Genetics and Genomics > 2018 > 45(7): 415-417

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WocEA: The visualization of functional enrichment results in word clouds

doi: 10.1016/j.jgg.2018.02.008

Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology and the Collaborative Innovation Center for Biomedical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China

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Corresponding author: E-mail address: dengwankun@hust.edu.cn (Wankun Deng); E-mail address: xueyu@hust.edu.cn (Yu Xue)
Received Date: 2017-08-22
Accepted Date: 2018-02-18
Rev Recd Date: 2018-02-06

Available Online: 2018-04-13

Publish Date: 2018-07-20

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References(12)

References

[1]	Baroukh, C., Jenkins, S.L., Dannenfelser, R. et al. Genes2WordCloud: a quick way to identify biological themes from gene lists and free text Source Code Biol. Med., 6 (2011),p. 15
[2]	Kolde, R., Vilo, J. GOsummaries: an R package for visual functional annotation of experimental data F1000 Res., 4 (2015),p. 574
[3]	Li, S., Shui, K., Zhang, Y. et al. CGDB: a database of circadian genes in eukaryotes Nucleic Acids Res., 45 (2017),pp. D397-D403
[4]	Oesper, L., Merico, D., Isserlin, R. et al. WordCloud: a Cytoscape plugin to create a visual semantic summary of networks Source Code Biol. Med., 6 (2011),p. 7
[5]	Ronningen, T., Shah, A., Oldenburg, A.R. et al. Prepatterning of differentiation-driven nuclear lamin A/C-associated chromatin domains by GlcNAcylated histone H2B Genome Res., 25 (2015),pp. 1825-1835
[6]	Supek, F., Bosnjak, M., Skunca, N. et al. REVIGO summarizes and visualizes long lists of gene ontology terms PLoS One, 6 (2011)
[7]	Tabas-Madrid, D., Nogales-Cadenas, R., Pascual-Montano, A. GeneCodis3: a non-redundant and modular enrichment analysis tool for functional genomics Nucleic Acids Res., 40 (2012),pp. W478-W483
[8]	Tavazoie, S., Hughes, J.D., Campbell, M.J. et al. Systematic determination of genetic network architecture Nat. Genet., 22 (1999),pp. 281-285
[9]	Viegas, F.B., Wattenberg, M., Feinberg, J. Participatory visualization with wordle IEEE Trans. Visual. Comput. Graph., 15 (2009),pp. 1137-1144
[10]	Villar, D., Berthelot, C., Aldridge, S. et al. Enhancer evolution across 20 mammalian species Cell, 160 (2015),pp. 554-566
[11]	Wadi, L., Meyer, M., Weiser, J. et al. Impact of outdated gene annotations on pathway enrichment analysis Br. J. Pharmacol., 13 (2016),pp. 705-706
[12]	Xue, Y., Wang, X. Bioinformaticians wrestling with the big biomedical data J. Genet. Genomics, 44 (2017),pp. 223-225