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Special Section Technical Briefs

Inferring Gene Regulatory Networks by Context Dependent and Independent Effects1

[+] Author and Article Information
Wuming Gong, Koyano-Nakagawa Naoko, Daniel J. Garry

Lillehei Heart Institute,
University of Minnesota,
Minneapolis, MN 55455

Accepted and presented at The Design of Medical Devices Conference (DMD2015), April 13–16, 2015, Minneapolis, MN, USA.

Manuscript received March 3, 2015; final manuscript received March 17, 2015; published online July 16, 2015. Editor: Arthur Erdman.

J. Med. Devices 9(3), 030947 (Sep 01, 2015) (3 pages) Paper No: MED-15-1103; doi: 10.1115/1.4030577 History: Received March 03, 2015; Revised March 17, 2015; Online July 16, 2015

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References

Nishiyama, A., Xin, L., Sharov, A. A., Thomas, M., Mowrer, G., Meyers, E., Piao, Y., Mehta, S., Yee, S., Nakatake, Y., Stagg, C., Sharova, L., Correa-Cerro, L. S., Bassey, U., Hoang, H., Kim, E., Tapnio, R., Qian, Y., Dudekula, D., Zalzman, M., Li, M., Falco, G., Yang, H.-T., Lee, S.-L., Monti, M., Stanghellini, I., Islam, M. N., Nagaraja, R., Goldberg, I., Wang, W., Longo, D. L., Schlessinger, D., and Ko, M. S. H., 2009, “Uncovering Early Response of Gene Regulatory Networks in ESCs by Systematic Induction of Transcription Factors,” Cell Stem Cell, 5(4), pp. 420–433. [CrossRef] [PubMed]
Yousefi, M., Hajihoseini, V., Jung, W., Hosseinpour, B., Rassouli, H., Lee, B., Baharvand, H., Lee, K., and Salekdeh, G. H., 2012, “Embryonic Stem Cell Interactomics: The Beginning of a Long Road to Biological Function,” Stem Cell Rev., 8(4), pp. 1138–1154. [CrossRef] [PubMed]
Zhang, J., Li, L., Peng, L., Sun, Y., and Li, J., 2013, “An Efficient Weighted Graph Strategy to Identify Differentiation Associated Genes in Embryonic Stem Cells,” PLoS One, 8(4), p. e62716. [CrossRef] [PubMed]
Schäfer, J., and Strimmer, K., 2005, “An Empirical Bayes Approach to Inferring Large-Scale Gene Association Networks,” Bioinformatics, 21(6), pp. 754–764. [CrossRef] [PubMed]
Huang, T., Liu, L., Qian, Z., Tu, K., Li, Y., and Xie, L., 2010, “Using GeneReg to Construct Time Delay Gene Regulatory Networks,” BMC Res. Notes, 3(1), pp. 142–151. [CrossRef] [PubMed]
Zoppoli, P., Morganella, S., and Ceccarelli, M., 2010, “TimeDelay-ARACNE: Reverse Engineering of Gene Networks From Time-Course Data by an Information Theoretic Approach,” BMC Bioinf., 11, pp. 154–168. [CrossRef]

Figures

Grahic Jump Location
Fig. 1

Modeling GRN of early ESC differentiation by NICE using temporal microarray dataset perturbing 50 TFs. ((a)–(c)) observed expression levels in Dox and Dox+ samples at 48 hrs for Pou5f1, Sox2, and T. ((d)–(f)) observed expression levels in Dox and predicted expression levels at 48 hrs for Pou5f1, Sox2, and T (cc: correlation coefficient).

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