Predicting gene expression from combined expression and promoter profile similarity with application to missing value imputation

Modeling and Simulation in Science, Engineering and Technology

Volumn 38, Issue , 2007, Pages 97-104

  Elo, Laura L ^a,b   Johannes, Tuikkala ^a   Nevalainen, Olli S ^a   Aittokallio, Tero ^a,b  

^a UNIVERSITY OF TURKU   (Finland)

^b TURKU CENTRE FOR BIOTECHNOLOGY   (Finland)

Author keywords

Gene expression; Imputation; Microarrays; Promoter sequence

Indexed keywords

EID: 85027978916     PISSN: 21643679     EISSN: 21643725     Source Type: Book Series    
DOI: 10.1007/978-0-8176-4558-8_9     Document Type: Chapter

References (14)

1. Allocco, D.J., Kohane, I.S., Butte, A.J.: Quantifying the relationship between co-expression, co-regulation and gene function. BMC Bioinformatics, 5, 18 (2004).
2. Altman, R.B., Raychaudhuri, S.: Whole-genome expression analysis: challenges beyond clustering. Curr. Opin. Struct. Biol., 11, 340–347 (2001).
3. Bar-Joseph, Z., Gerber, G.K., Lee, T.I., Rinaldi, N.J., You, J.Y., Robert, F., et al.: Computational discovery of gene modules and regulatory networks. Nat. Biotechnol., 21, 1337–1342 (2003).
4. De Brevern, A.G., Hazout, S., Malpertuy, A.: Influence of microarrays experiments missing values on the stability of gene groups by hierarchical clustering. BMC Bioinformatics, 5, 114 (2004).
5. DeRisi, J.L., Iyer, V.R., Brown, P.O.: Exploring the metabolic and genetic control of gene expression on a genomic scale. Science, 278, 680–686 (1997).
6. Gasch, A.P., Spellman, P.T., Kao, C.M., Carmel-Harel, O., Eisen, M.B., Storz, G., et al.: Genomic expression program in the response of yeast cells to environmental changes. Mol. Biol. Cell, 11, 4241–4257 (2000).
7. Glenisson, P., Mathys, J., De Moor, B.: Meta-clustering of gene expression data and literature-based information. SIGKDD Explorations, 5, 101–112 (2003).
8. Hanisch, D., Zien, A., Zimmer, R., Lengauer, T.: Co-clustering of biological networks and gene expression data. Bioinformatics, 18, S145–S154 (2002).
9. Kim, H., Golub, G.H., Park, H.: Missing value estimation for DNA microarray gene expression data: local least squares imputation. Bioinformatics, 21, 187–198 (2005).
10. Lapidot, M., Pilpel, Y.: Comprehensive quantitative analyses of the effects of promoter sequence elements on mRNA transcription. Nucleic Acids Res., 31, 3824–3828 (2003).
11. Lee, T.I., Rinaldi, N.J., Robert, F., Odom, D.T., Bar-Joseph, Z., Gerber, G.K., et al.: Transcriptional regulatory networks in Saccharomyces cerevisiae. Science, 298, 799–804 (2002).
12. Spellman, P.T., Sherlock, G., Zhang, M.Q., Iyer, V.R., Anders, K., Eisen, M.B., et al.: Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol. Biol. Cell, 9, 3273–3297 (1998).
13. Tavazoie, S., Hughes, J.D., Campbell, M.J., Cho, R.J., Church, G.M.: Systematic determination of genetic network architecture. Nat. Genet., 22, 281–285 (1999).
14. Troyanskaya, O., Cantor, M., Sherlock, G., Brown, P., Hastie, T., Tibshirani, R., et al.: Missing value estimation methods for DNA microarrays. Bioinformatics, 17, 520–525 (2001).