Gavin Sherlock
November 11, 2008
Literature References
Clustering
Eisen
MB, Spellman PT, Brown PO, Botstein D. (1998). Cluster analysis and
display of genome-wide expression patterns. Proc Natl Acad Sci U S A
95(25):14863-8.
Tamayo P, Slonim D, Mesirov J, Zhu Q, Kitareewan S, Dmitrovsky E,
Lander ES, Golub TR (1999). Interpreting patterns of gene expression
with self-organizing maps: methods and application to hematopoietic
differentiation. Proc Natl Acad Sci USA 96(6):2907.
Tavazoie
S, Hughes JD, Campbell MJ, Cho RJ, Church GM (1999). Systematic
determination of genetic network architecture. Nat Genet.
22(3):281-5.
Tusher
VG, Tibshirani R, Chu G (2001). Significance analysis of microarrays
applied to the ionizing radiation response. Proc Natl Acad Sci USA
98(9):5116-21.
Slonim
DK. (2002). From patterns to pathways: gene expression data analysis
comes of age. Nat Genet. 32 Suppl:502-8.
McShane
LM, Radmacher MD, Freidlin B, Yu R, Li MC, Simon R. (2002). Methods
for assessing reproducibility of clustering patterns observed in
analyses of microarray data. Bioinformatics
18(11):1462-9.
Bryan
J (2004). Problems in gene clustering based on gene expression data.
Journal of Multivariate Analysis 90, 44-66.
D'haeseleer
P (2005). How does gene expression clustering work? Nat Biotechnol.
23(12):1499-501.
Chipman
H and Tibshirani R (2006). Hybrid Hierarchical Clustering with
Applications to Microarray Data. Biostatistics,
7(2):286-301.
Cluster Validation and Analysis
Ben-Hur,
A., Elisseeff, A., & Guyon, I. (2002, 2002). A stability based method
for discovering structure in clustered data. Paper presented at the
Pac Symp Biocomput.
Yeung
KY, Haynor DR, Ruzzo WL. (2001). Validating clustering for gene
expression data. Bioinformatics 17, 309-318.
Gibbons
FD, Roth FP. (2002). Judging the quality of gene expression-based
clustering methods using gene annotation. Genome Res.
12(10):1574-81.
Slonim
DK. (2002). From patterns to pathways: gene expression data analysis
comes of age. Nat Genet. 32 Suppl:502-8.
McShane
LM, Radmacher MD, Freidlin B, Yu R, Li MC, Simon R. (2002). Methods
for assessing reproducibility of clustering patterns observed in
analyses of microarray data. Bioinformatics
18(11):1462-9.
Zhou
X, Kao MC, Wong WH. (2002). Transitive functional annotation by
shortest-path analysis of gene expression data. Proc Natl Acad Sci U
S A. 99(20):12783-8.
Mootha
VK, Lindgren CM, Eriksson KF, Subramanian A, Sihag S, Lehar J,
Puigserver P, Carlsson E,
Ridderstrale M, Laurila E, Houstis N, Daly MJ, Patterson N, Mesirov
JP, Golub TR, Tamayo P, Spiegelman B, Lander ES, Hirschhorn JN,
Altshuler D, Groop LC. (2003). PGC-1alpha-responsive
genes involved in oxidative phosphorylation are coordinately
downregulated in human diabetes. Nat Genet. 34, 267-73.
Breitling
R, Amtmann A, Herzyk P (2004). Iterative Group Analysis (iGA): a
simple tool to enhance sensitivity and facilitate interpretation of
microarray experiments. BMC Bioinformatics 5(1):34.
Boyle
EI, Weng S, Gollub J, Jin H, Botstein D, Cherry JM, Sherlock G
(2004). GO::TermFinder--open source software for accessing Gene
Ontology information and finding significantly enriched Gene Ontology
terms associated with a list of genes. Bioinformatics.
20(18):3710-5.
Subramanian
A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, Paulovich
A, Pomeroy SL, Golub TR, Lander ES, Mesirov JP (2005). Gene set
enrichment analysis: a knowledge-based approach for interpreting
genome-wide expression profiles. Proc Natl Acad Sci U S A. 102,
15545-50.
Handl
J, Knowles J, Kell DB (2005). Computational cluster validation in
post-genomic data analysis. Bioinformatics.
21(15):3201-12.
