Abstract
The advent of high-throughput techniques is transforming biology into a data rich field. A variety of genomics data is now available, each providing a different perspective of gene regulation. Even though each type of data requires specific computational methods, methods that combine complimentary datasets are necessary to obtain additional information that is not available by analyzing the either of the dataset alone. In this paper, we propose a Bayesian approach to integrate gene expression data with genome-wide protein-DNA interaction data. The proposed method combines these datasets in order to probabilistic predict transcription factors for genes. We evaluate the proposed method using SaccharomycesCerevisiae Cell Cycle data. Results are compared with that of previous method.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Lee, T.I., Young, R.A.: Transcription of eukaryotic protein-coding genes. Annu. Rev. Genet. 34, 77–137 (2000)
Eisen, M.B., Spellman, P.T., Brown, P.O., Botstein, D.: Cluster analysis and display of genome-wide expression patterns. Proc. Natl. Acad. Sci. USA 95, 14863–14868 (1998)
Tamayo, P., Slonim, D., Mesirov, J., Zhu, Q., Kitareewan, S., Dmitrovsky, E., Lander, E.S., Golub, T.R.: Interpreting patterns of gene expression with self-organizing maps: methods and application to hematopoietic differentiation. Proc. Natl. Acad. Sci. USA 96, 2907–2912 (1999)
Tavazoie, S., Huges, J.D., Campbell, M.J., Cho, R.J., Church, G.M.: Systematic determination of genetic network architecture. Nat. Genet. 22, 281–285 (1999)
Bar-Joseph, Z., Gerber, G.K., Lee, T.I., Rinaldi, N.J., Yoo, J.Y., Robert, F., Gordon, D.B., Fraenkel, E., Jaakkola, T.S., Young, R.A., Gifford, D.K.: Computational discovery of gene modules and regulatory networks. Nat. Biotechnol. 21, 1337–1342 (2003)
Segal, E., Shapira, M., Regev, A., Peer, D., Bostein, D., Koller, D., Friedman, N.: Module networks: identifying regulatory modules and their condition- specific regulators from gene expression data. Nat. Genet. 34, 166–176 (2003)
Ren, B., Robert, F., Wyrick, J., Aparicio, O., Jennings, E., Simon, I., Zeitlinger, J., Schreiber, J., Hannett, N., Kanin, E., Volkert, T., Wilson, C.J., Bell, S.P., Young, R.A.: Genome-wide location and function of DNA binding proteins. Science 290, 2306–2309 (2000)
Iyer, V.R., Horak, C.E., Scafe, C.S., Botstein, D., Snyder, M., Brown, P.O.: Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF. Nature 409, 533–538 (2001)
Simon, I., Barnett, J., Hannett, N., Harbison, C.T., Rinaldi, N.J., Volkert, T.L., Wyrick, J.J., Zeitlinger, J., Gifford, D.K., Jaakkola, T.S., Young, R.A.: Serial regulation of transcriptional regulators in the yeast cell cycle. Cell 106, 697–708 (2001)
Futcher, B.: Transcriptional regulatory networks and the yeast cell cycle. Curr. Opin. Cell. Biol. 14, 676–683 (2002)
Hartemink, A.J., Gifforf, D.K., Jaakkola, T.S., Young, R.A.: Combining location and expression data for principled discovery of genetic regulatory network models. In: Pacific Symposium on Biocomputing, pp. 437–449 (2002)
Duda, R.O, Hart, M.P: Pattern classification and scene analysis. Wiley, New York (1973)
Spellman, P.T., Sherlock, G., Zhang, M.Q., Iyer, V.R., Anders, K., Eisen, M.B., Brown, P.O., Botstein, D., Futcher, B.: Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol. Biol. Cell 9, 3273–3297 (1998)
Jackson, J.E.: A User’s Guide to Principal Components. John Wiley, New York (1991)
Koranda, M., Schleiffer, A., Endler, L., Ammerer, G.: Fork-head-like transcription factors recruit Ndd1 to the chromatin of G2/M-specific promoters. Nature 406, 94–98 (2000)
Zhu, G., Spellman, P.T., Volpe, T., Brown, P.O., Botstein, D., Davis, T.N., Futcher, B.: Two yeast forkhead genes regulate the cell cycle and pseudohyphal growth. Nature 406, 90–94 (2000)
Author information
Authors and Affiliations
Editor information
Rights and permissions
Copyright information
© 2007 Springer Berlin Heidelberg
About this paper
Cite this paper
Jonnalagadda, S., Srinivasan, R. (2007). A Bayesian Approach for Integrating Transcription Regulation and Gene Expression: Application to Saccharomyces Cerevisiae Cell Cycle Data. In: Eskin, E., Ideker, T., Raphael, B., Workman, C. (eds) Systems Biology and Regulatory Genomics. RSB RRG 2005 2005. Lecture Notes in Computer Science(), vol 4023. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-48540-7_15
Download citation
DOI: https://doi.org/10.1007/978-3-540-48540-7_15
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-48293-2
Online ISBN: 978-3-540-48540-7
eBook Packages: Computer ScienceComputer Science (R0)