Abstract
Recently, the reconstruction of co-regulated gene network has become increasingly popular in the area of bioinformatics. It tries to find the associated information and network topology among genes through large numbers of biological data. In this paper, we proposed a novel method PC-GO by using path consistency (PC) algorithm based on gene ontology (GO). GO provides a basis for measuring the conditional semantic similarity between genes, and then PC algorithm is applied to remove links between genes with less correlation in the network. We successfully applied our algorithm to yeast data. Experimental results show that the accuracy and integrity of the co-regulated network acquired by our method outperforms previous methods.
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Obayashi, T., et al.: ATTED-II: a database of co-expressed genes and cis elements for identifying co-regulated gene groups in Arabidopsis. Nucleic Acids Research 35(suppl. 1), D863–D869 (2007)
Lanctôt, C., et al.: Dynamic genome architecture in the nuclear space: regulation of gene expression in three dimensions. Nature Reviews Genetics 8(2), 104–115 (2007)
Korbel, J.O., et al.: Systematic association of genes to phenotypes by genome and literature mining. PLoS Biology 3(5), e134 (2005)
Lee, I., et al.: Rational association of genes with traits using a genome-scale gene network for Arabidopsis thaliana. Nature Biotechnology 28(2), 149–156 (2010)
Perez-Iratxeta, C., Bork, P., Andrade, M.A.: Association of genes to genetically inherited diseases using data mining. Nature Genetics 31(3), 316–319 (2002)
Berri, S., et al.: Characterization of WRKY co-regulatory networks in rice and Arabidopsis. BMC Plant Biology 9(1), 120 (2009)
Teichmann, S.A., Babu, M.M.: Conservation of gene co-regulation in prokaryotes and eukaryotes. Trends in Biotechnology 20(10), 407–410 (2002)
Ashburner, M., et al.: Gene Ontology: tool for the unification of biology. Nature Genetics 25(1), 25–29 (2000)
Wei, H., et al.: Transcriptional coordination of the metabolic network in Arabidopsis. Plant Physiology 142(2), 762–774 (2006)
Wang, J.Z., et al.: A new method to measure the semantic similarity of GO terms. Bioinformatics 23(10), 1274–1281 (2007)
Teixeira, M.C., et al.: The YEASTRACT database: a tool for the analysis of transcription regulatory associations in Saccharomyces cerevisiae. Nucleic Acids Research 34(suppl. 1), D446–D451 (2006)
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Wang, H., Wang, C., Liu, L., Du, C., Lu, J. (2014). Identification of Co-regulated Gene Network by Using Path Consistency Algorithm Based on Gene Ontology. In: Shi, Z., Wu, Z., Leake, D., Sattler, U. (eds) Intelligent Information Processing VII. IIP 2014. IFIP Advances in Information and Communication Technology, vol 432. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-662-44980-6_31
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DOI: https://doi.org/10.1007/978-3-662-44980-6_31
Publisher Name: Springer, Berlin, Heidelberg
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