Supplemental material for O. Alter and G. H. Golub, "Integrative Analysis of Genome-Scale Data Using Pseudoinverse Projection Predicts Novel Correlation Between DNA Replication and RNA Transcription," Proceedings of the National Academy of Sciences 101 (47), pp. 16577–16582 (November 2004).
A PDF format file, readable by Adobe Acrobat Reader.
- PNAS_2004.pdf
A PDF format file, readable by Adobe Acrobat Reader.
- PNAS_2004_Appendix.pdf
Mathematica 5.0 code files, executable by Mathematica 5.0 and readable by the
freely available MathReader.
PDF format files, readable by Adobe Acrobat Reader.
Tab-delimited text format files, readable by both Mathematica and Microsoft Excel.
Yeast RNA Expression Dataset For SVD Basis Computation
- Reproduced from P. T. Spellman, G. Sherlock, M. Q. Zhang, V. R. Iyer, K. Anders, M. B. Eisen, P. O. Brown, D. Botstein and B. Futcher, "Comprehensive Identification of Cell Cycle-Regulated Genes of the Yeast Saccharomyces cerevisiae by Microarray Hybridization,"
Molecular Biology of the Cell 9 (12), pp. 3273–3297 (December 1998);
and from O. Alter, P. O. Brown and D. Botstein, "Singular Value Decomposition for Genome-Wide Expression Data Processing and Modeling," Proceedings of the National Academy of Sciences 97 (18), pp. 10101–10106 (August 2000).
Classification List of Yeast Cell Cycle-Regulated Genes
- Reproduced from P. T. Spellman, G. Sherlock, M. Q. Zhang, V. R. Iyer, K. Anders, M. B. Eisen, P. O. Brown, D. Botstein and B. Futcher, "Comprehensive Identification of Cell Cycle-Regulated Genes of the Yeast Saccharomyces cerevisiae by Microarray Hybridization,"
Molecular Biology of the Cell 9 (12), pp. 3273–3297 (December 1998).
Yeast and Human RNA Expression Datasets For GSVD Basis Computation
- Reproduced from P. T. Spellman, G. Sherlock, M. Q. Zhang, V. R. Iyer, K. Anders, M. B. Eisen, P. O. Brown, D. Botstein and B. Futcher, "Comprehensive Identification of Cell Cycle-Regulated Genes of the Yeast Saccharomyces cerevisiae by Microarray Hybridization,"
Molecular Biology of the Cell 9 (12), pp. 3273–3297 (December 1998);
M. L. Whitfield, G. Sherlock, A. Saldanha, J. I. Murray, C. A. Ball, K. E. Alexander, J. C. Matese, C. M. Perou, M. M. Hurt, P. O. Brown and D. Botstein, "Identification of Genes Periodically Expressed in the Human Cell Cycle and their Expression in Tumors,"Molecular Biology of the Cell 13 (6), pp. 1977–2000 (June 2002);
and from O. Alter, P. O. Brown and D. Botstein, "Generalized Singular Value Decomposition for Comparative Analysis of Genome-Scale Expression Datasets of Two Different Organisms," Proceedings of the National Academy of Sciences 100 (6), pp. 3351–3356 (March 2003).
Yeast Proteins' DNA-Binding Dataset For Pseudoinverse Projection Integration With the SVD and GSVD RNA Expression Bases
- Reproduced from
I. Simon, J. Barnett, N. Hannett, C. T. Harbison, N. J. Rinaldi, T. L. Volkert, J. J. Wyrick, J. Zeitlinger, D. K. Gifford, T. S. Jaakkola and R. A. Young, "Serial Regulation of Transcriptional Regulators in the Yeast Cell Cycle,"
Cell 106 (6), pp. 697–708 (September 2001);
and from J. J. Wyrick, J. G. Aparicio, T. Chen, J. D. Barnett, E. G. Jennings, R. A. Young, S. P. Bell and O. M. Aparicio, "Genome-Wide Distribution of ORC and MCM Proteins in S. cerevisiae: High-Resolution Mapping of Replication Origins by Microarray Hybridization,"Science 294 (5550), pp. 2357–2360 (December 2001).
Yeast RNA Expression Datasets For Pseudoinverse Projection Integration With the SVD and GSVD RNA Expression Bases
- Reproduced from P. T. Spellman, G. Sherlock, M. Q. Zhang, V. R. Iyer, K. Anders, M. B. Eisen, P. O. Brown, D. Botstein and B. Futcher, "Comprehensive Identification of Cell Cycle-Regulated Genes of the Yeast Saccharomyces cerevisiae by Microarray Hybridization,"
Molecular Biology of the Cell 9 (12), pp. 3273–3297 (December 1998).