Gene network inference and visualization tools for biologists: Application to new human transcriptome datasets

Daniel Hurley; Hiromitsu Araki; Yoshinori Tamada; Ben Dunmore; Deborah Sanders; Sally Humphreys; Muna Affara; Seiya Imoto; Kaori Yasuda; Yuki Tomiyasu; Kosuke Tashiro; Christopher Savoie; Vicky Cho; Stephen Smith; Satoru Kuhara; Satoru Miyano; D. Stephen Charnock-Jones; Edmund J. Crampin; Cristin G. Print

doi:10.1093/nar/gkr902

Gene network inference and visualization tools for biologists: Application to new human transcriptome datasets

Daniel Hurley, Hiromitsu Araki, Yoshinori Tamada, Ben Dunmore, Deborah Sanders, Sally Humphreys, Muna Affara, Seiya Imoto, Kaori Yasuda, Yuki Tomiyasu, Kosuke Tashiro, Christopher Savoie, Vicky Cho, Stephen Smith, Satoru Kuhara, Satoru Miyano, D. Stephen Charnock-Jones, Edmund J. Crampin, Cristin G. Print

Research output: Contribution to journal › Article

38 Citations (Scopus)

Abstract

Gene regulatory networks inferred from RNA abundance data have generated significant interest, but despite this, gene network approaches are used infrequently and often require input from bioinformaticians. We have assembled a suite of tools for analysing regulatory networks, and we illustrate their use with microarray datasets generated in human endothelial cells. We infer a range of regulatory networks, and based on this analysis discuss the strengths and limitations of network inference from RNA abundance data. We welcome contact from researchers interested in using our inference and visualization tools to answer biological questions.

Original language	English
Pages (from-to)	2377-2398
Number of pages	22
Journal	Nucleic acids research
Volume	40
Issue number	6
DOIs	https://doi.org/10.1093/nar/gkr902
Publication status	Published - Mar 1 2012

All Science Journal Classification (ASJC) codes

Genetics

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10.1093/nar/gkr902

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Hurley, D., Araki, H., Tamada, Y., Dunmore, B., Sanders, D., Humphreys, S., Affara, M., Imoto, S., Yasuda, K., Tomiyasu, Y., Tashiro, K., Savoie, C., Cho, V., Smith, S., Kuhara, S., Miyano, S., Charnock-Jones, D. S., Crampin, E. J., & Print, C. G. (2012). Gene network inference and visualization tools for biologists: Application to new human transcriptome datasets. Nucleic acids research, 40(6), 2377-2398. https://doi.org/10.1093/nar/gkr902

Gene network inference and visualization tools for biologists : Application to new human transcriptome datasets. / Hurley, Daniel; Araki, Hiromitsu; Tamada, Yoshinori; Dunmore, Ben; Sanders, Deborah; Humphreys, Sally; Affara, Muna; Imoto, Seiya; Yasuda, Kaori; Tomiyasu, Yuki; Tashiro, Kosuke; Savoie, Christopher; Cho, Vicky; Smith, Stephen; Kuhara, Satoru; Miyano, Satoru; Charnock-Jones, D. Stephen; Crampin, Edmund J.; Print, Cristin G.

In: Nucleic acids research, Vol. 40, No. 6, 01.03.2012, p. 2377-2398.

Research output: Contribution to journal › Article

Hurley, D, Araki, H, Tamada, Y, Dunmore, B, Sanders, D, Humphreys, S, Affara, M, Imoto, S, Yasuda, K, Tomiyasu, Y, Tashiro, K, Savoie, C, Cho, V, Smith, S, Kuhara, S, Miyano, S, Charnock-Jones, DS, Crampin, EJ & Print, CG 2012, 'Gene network inference and visualization tools for biologists: Application to new human transcriptome datasets', Nucleic acids research, vol. 40, no. 6, pp. 2377-2398. https://doi.org/10.1093/nar/gkr902

Hurley, Daniel ; Araki, Hiromitsu ; Tamada, Yoshinori ; Dunmore, Ben ; Sanders, Deborah ; Humphreys, Sally ; Affara, Muna ; Imoto, Seiya ; Yasuda, Kaori ; Tomiyasu, Yuki ; Tashiro, Kosuke ; Savoie, Christopher ; Cho, Vicky ; Smith, Stephen ; Kuhara, Satoru ; Miyano, Satoru ; Charnock-Jones, D. Stephen ; Crampin, Edmund J. ; Print, Cristin G. / Gene network inference and visualization tools for biologists : Application to new human transcriptome datasets. In: Nucleic acids research. 2012 ; Vol. 40, No. 6. pp. 2377-2398.

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