Utilizing cis-elements to refine gene regulatory networks

Yiou Xiao, Kishan Mehrotra, Chilukuri K Mohan, Ramesh Raina

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

Gene regulatory networks (GRNs) describe epistatic relationship of genes and how the expression of some genes influence the expression of other genes. This information is critical for understanding molecular mechanisms regulating various biological processes and molecular basis of several diseases. Current research work mostly attempts to infer such regulatory relationships (and GRN architecture topology) from gene expression data. This paper improves on this methodology by utilizing additional information available that describes which cis-elements are present in which genes, and at what locations. Using the underlying principle that target genes of a transcription factor should share the same binding site in their promoter regions, we propose a scoring method that facilitates the refinement of a candidate GRN. Improvements are demonstrated with three data sets, on which GRNs are first obtained from existing dataset (AtRegNet) or using an existing approach (ARACNe), and then modified using cis-element information.

Original languageEnglish (US)
Title of host publicationProceedings - 2013 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2013
Pages65-71
Number of pages7
DOIs
StatePublished - 2013
Event2013 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2013 - Shanghai, China
Duration: Dec 18 2013Dec 21 2013

Other

Other2013 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2013
CountryChina
CityShanghai
Period12/18/1312/21/13

Fingerprint

Genes
Transcription factors
Binding sites
Network architecture
Gene expression
Topology

Keywords

  • Cis-element
  • Gene Regulatory Network
  • Motif
  • Transcription Factor

ASJC Scopus subject areas

  • Biomedical Engineering

Cite this

Xiao, Y., Mehrotra, K., Mohan, C. K., & Raina, R. (2013). Utilizing cis-elements to refine gene regulatory networks. In Proceedings - 2013 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2013 (pp. 65-71). [6732737] https://doi.org/10.1109/BIBM.2013.6732737

Utilizing cis-elements to refine gene regulatory networks. / Xiao, Yiou; Mehrotra, Kishan; Mohan, Chilukuri K; Raina, Ramesh.

Proceedings - 2013 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2013. 2013. p. 65-71 6732737.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Xiao, Y, Mehrotra, K, Mohan, CK & Raina, R 2013, Utilizing cis-elements to refine gene regulatory networks. in Proceedings - 2013 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2013., 6732737, pp. 65-71, 2013 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2013, Shanghai, China, 12/18/13. https://doi.org/10.1109/BIBM.2013.6732737
Xiao Y, Mehrotra K, Mohan CK, Raina R. Utilizing cis-elements to refine gene regulatory networks. In Proceedings - 2013 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2013. 2013. p. 65-71. 6732737 https://doi.org/10.1109/BIBM.2013.6732737
Xiao, Yiou ; Mehrotra, Kishan ; Mohan, Chilukuri K ; Raina, Ramesh. / Utilizing cis-elements to refine gene regulatory networks. Proceedings - 2013 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2013. 2013. pp. 65-71
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