R: R Development Core Team (2008). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0, URL http://www.R-project.org
affy package for CEL files preprocessing: Gautier, L., Cope, L., Bolstad, B. M., and Irizarry, R. A. 2004. affy---analysis of Affymetrix GeneChip data at the probe level. Bioinformatics 20, 3 (Feb. 2004), 307-315
aroma.affymetrix package for CEL files preprocessing:
H. Bengtsson; K. Simpson; J. Bullard; K. Hansen. aroma.affymetrix: A generic framework in R for analyzing small to very large Affymetrix data sets in bounded memory, Tech Report #745, Department of Statistics, University of California, Berkeley, February 2008
H. Bengtsson, R. Irizarry, B. Carvalho, & T.P. Speed. Estimation and assessment of raw copy numbers at the single locus level, Bioinformatics, 2008
gcrma R package: Jean(ZHIJIN) Wu and Rafael Irizarry with contributions from James MacDonald Jeff Gentry (). gcrma: Background Adjustment Using Sequence Information. R package version 2.14.1.
Quantile normalization: Bolstad, B. M. Irizarry, R. A. Astrand, M. and Speed, T. P. A Comparison of Normalization Methods for High Density Oligonucleotide Array Data Based on Variance and Bias. Bioinformatics 19(2):185-193, 2003
Non-linear baseline normalization: Schadt, E., C. Li, B. Eliss, and W. H. Wong. Feature extraction and normalization algorithms for high-density oligonucleotide gene expression array data. J. Cell. Biochem. 84(S37),120–125, 2002
SAM (Significance Analysis of Microarray):
V. Tusher., R. Tibshirani., and G. Chu. Significance analysis of microarrays applied to the ionizing radiation response. PNAS, 98: 5116-5121, 2001
R. Tibshirani, G. Chu, T. Hastie and Balasubramanian Narasimhan (). samr: SAM: Significance Analysis of Microarrays. R package version 1.26. http://www-stat.stanford.edu/~tibs/SAM
K-Means clustering algorithm: Tavazoie, S., Hughes, J. D., Campbell, M. J., Cho, R. J., and Church, G. M. Systematic determination of genetic network architecture. Nat Genet, 22: 281-285, 1999
SOM clustering algorithm: Tamayo, P., Slonim, D., Mesirov, J., Zhu, Q., Kitareewan, S., Dmitrovsky, E., Lander, E. S., and Golub, T. R. Interpreting patterns of gene expression with self-organizing maps: methods and application to hematopoietic differentiation. Proc Natl Acad Sci U S A, 96, 2907-2912, 1999
CLICK clustering algorithm: Sharan, R. and Shamir, R. CLICK: a clustering algorithm with applications to gene expression analysis. Proc Int Conf Intell Syst Mol Biol 8, 307-16, 2000
SAMBA biclustering algorithm: Tanay, A. Sharan, R. and Shamir, R. Discovering statistically significant biclusters in gene expression data. Bioinformatics, 18(1), 136-144, 2002
Matisse network grouping: Ulitsky, I. and Shamir, R. MATISSE: Identification of functional modules using network topology and high-throughput data. BMC Systems Biology, vol 1, No. 8 (2007)
Context Scores for miRNA enrichment analysis: Grimson, A., Kai-How Farh, F. K Johnston, W., Garrett-Engele, F., P Lim, L., P Bartel, D. MicroRNA Targeting Specificity in Mammals: Determinants beyond Seed Pairing. Molecular Cell, 27:91-105 (2007)
PRIMA algorithm: Elkon, R., Linhart, C. Sharan, R. Samir, R. and Shiloh, Y. Genome-Wide In Silico Identification of Transcriptional Regulators Controlling the Cell Cycle in Human Cells. Genome Research, Vol. 13(5), pp. 773-780, 2003.
Spike software and DB: R. Elkon, R. Vesterman, N. Amit, I. Ulitsky, I. Zohar, M. Weisz, G. Mass, N. Orlev, G. Sternberg, R. Blekhman, J. Assa, Y. Shiloh and R.Shamir. SPIKE - a database, visualization and analysis tool of cellular signaling pathways. BMC Bioinformatics 2008, 9:11
Spike home page: http://www.cs.tau.ac.il/~spike/
Agglomerative algorithm for hierarchical clustering: Eisen, M. B., Spellman, P. T. et al. Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci U S A 95(25), 14863-8, 1998
TF binding site profiles that were used to generate the supplied yeast TF fingerprint files: Harbison, C.T., D.B. Gordon, T.I. Lee, N.J. Rinaldi, K.D. Macisaac, T.W. Danford, N.M. Hannett, J.B. Tagne, D.B. Reynolds, J. Yoo, E.G. Jennings, J. Zeitlinger, D.K. Pokholok, M. Kellis, P.A. Rolfe, K.T. Takusagawa, E.S. Lander, D.K. Gifford, E. Fraenkel, and R.A. Young. Transcriptional regulatory code of a eukaryotic genome. Nature 431: 99-104, 2004
expressionData1.txt sample input file: Spellman, P. T., Sherlock, G., et al. Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol Biol Cell 9(12), 3273-97, 1998