-
1
-
-
60149104156
-
A statistical framework for testing functional categories in microarray data
-
Barry, W. T., Nobel, A. B., and Wright, F. A. (2008). A statistical framework for testing functional categories in microarray data. Annals of Applied Statistics 2, 286-315.
-
(2008)
Annals of Applied Statistics
, vol.2
, pp. 286-315
-
-
Barry, W.T.1
Nobel, A.B.2
Wright, F.A.3
-
2
-
-
0001028358
-
An inverse matrix adjustment arising in discriminant analysis
-
Bartlett, M. S. (1951). An inverse matrix adjustment arising in discriminant analysis. Annals of Mathematical Statistics 22, 107-111.
-
(1951)
Annals of Mathematical Statistics
, vol.22
, pp. 107-111
-
-
Bartlett, M.S.1
-
3
-
-
32644460955
-
Linear modelling of Pearson's product moment correlation coefficient: an application of Fisher's z-transformation
-
Bartlett, R. F. (1993). Linear modelling of Pearson's product moment correlation coefficient: an application of Fisher's z-transformation. Journal of the Royal Statistical Society, Series D 42, 45-53.
-
(1993)
Journal of the Royal Statistical Society, Series D
, vol.42
, pp. 45-53
-
-
Bartlett, R.F.1
-
6
-
-
0037316303
-
A comparison of normalization methods for high density oligonucleotide array data based on bias and variance
-
Bolstad, B. M., Irizarry, R. A., Astrand, M., and Speed, T. P. (2003). A comparison of normalization methods for high density oligonucleotide array data based on bias and variance. Bioinformatics 19, 185-193.
-
(2003)
Bioinformatics
, vol.19
, pp. 185-193
-
-
Bolstad, B.M.1
Irizarry, R.A.2
Astrand, M.3
Speed, T.P.4
-
7
-
-
0036401627
-
Bayesian hierarchical model for identifying changes in gene expression from microarray experiments
-
Broet, P., Richardson, S., and Radvanyi, F. (2002). Bayesian hierarchical model for identifying changes in gene expression from microarray experiments. Journal of Computational Biology 9, 671-683.
-
(2002)
Journal of Computational Biology
, vol.9
, pp. 671-683
-
-
Broet, P.1
Richardson, S.2
Radvanyi, F.3
-
8
-
-
0033901471
-
Bcl-2 and p53 protein expression, apoptosis, and p53 mutation in human epithelial ovarian cancers
-
Chan, W.-W., Cheung, K.-K., Schorge, J. O., Huang, L.-W., Welch, W. R., Bell, D. A., Berkowitz, R. S. and Mok, S. C. (2000). Bcl-2 and p53 protein expression, apoptosis, and p53 mutation in human epithelial ovarian cancers. Americal Journal of Pathology 156, 409-417.
-
(2000)
Americal Journal of Pathology
, vol.156
, pp. 409-417
-
-
Chan, W.-W.1
Cheung, K.-K.2
Schorge, J.O.3
Huang, L.-W.4
Welch, W.R.5
Bell, D.A.6
Berkowitz, R.S.7
Mok, S.C.8
-
9
-
-
28944444652
-
Differential coexpression analysis using microarray data and its application to human cancer
-
Choi, J. K., Yu, U., Yoo, O. J., and Kim, S. (2005). Differential coexpression analysis using microarray data and its application to human cancer. Bioinformatics 21, 4348-4355.
-
(2005)
Bioinformatics
, vol.21
, pp. 4348-4355
-
-
Choi, J.K.1
Yu, U.2
Yoo, O.J.3
Kim, S.4
-
10
-
-
77953913791
-
From 'differential expression' to 'differential networking'-identification of dysfunctional regulatory networks in diseases
-
de la Fuente, A. (2010). From 'differential expression' to 'differential networking'-identification of dysfunctional regulatory networks in diseases. Trends in Genetics 26, 326-333.
-
(2010)
Trends in Genetics
, vol.26
, pp. 326-333
-
-
de la Fuente, A.1
-
11
-
-
0002629270
-
Maximum likelihood from incomplete data via the em algorithm
-
Dempster, A. P., Laird, N. M., and Rubin, D. B. (1977). Maximum likelihood from incomplete data via the em algorithm. Journal of the Royal Statistical Society, Series B 39, 1-38.
-
(1977)
Journal of the Royal Statistical Society, Series B
, vol.39
, pp. 1-38
-
-
Dempster, A.P.1
Laird, N.M.2
Rubin, D.B.3
-
12
-
-
0001727379
-
The general sampling distribution of the multiple correlation coefficient
-
Fisher, R. A. (1928). The general sampling distribution of the multiple correlation coefficient. Journal of the Royal Statistical Society, Series A 121, 654-673.
-
(1928)
Journal of the Royal Statistical Society, Series A
, vol.121
, pp. 654-673
-
-
Fisher, R.A.1
-
14
-
-
85153156049
-
-
MCLUST version 3 for R: Normal mixture modeling and model-based clustering (revised 2009). Technical Report 504, Department of Statistics, University of Washington, Seattle, WA.
-
Fraley, C. and Raftery, A. E. (2006). MCLUST version 3 for R: Normal mixture modeling and model-based clustering (revised 2009). Technical Report 504, Department of Statistics, University of Washington, Seattle, WA
-
(2006)
-
-
Fraley, C.1
Raftery, A.E.2
-
15
-
-
69449083058
-
Candidate pathways and genes for prostate cancer: A meta-analysis of gene-expression data
-
Gorlov, I. P., Byun, J., Gorlova, O. Y., Aparicio, A. M., Efstathiou, E., and Logothetis, C. J. (2009). Candidate pathways and genes for prostate cancer: A meta-analysis of gene-expression data. BMC Medical Genomics 2, 48.
-
(2009)
BMC Medical Genomics
, vol.2
, pp. 48
-
-
Gorlov, I.P.1
Byun, J.2
Gorlova, O.Y.3
Aparicio, A.M.4
Efstathiou, E.5
Logothetis, C.J.6
-
17
-
-
62749083987
-
Detecting intergene correlation changes in microarray analysis: A new approach to gene selection
-
Hu, R., Qiu, X., Glazko, G., Klebanov, L., and Yakovlev, A. (2009). Detecting intergene correlation changes in microarray analysis: A new approach to gene selection. BMC Bioinformatics 10, 20.
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 20
-
-
Hu, R.1
Qiu, X.2
Glazko, G.3
Klebanov, L.4
Yakovlev, A.5
-
18
-
-
77949517089
-
A new gene selection procedure based on the covariance distance
-
Hu, R., Qiu, X., and Glazko, G. (2010). A new gene selection procedure based on the covariance distance. Bioinformatics 26, 348-354.
-
(2010)
Bioinformatics
, vol.26
, pp. 348-354
-
-
Hu, R.1
Qiu, X.2
Glazko, G.3
-
19
-
-
12344280017
-
Summaries of Affymetrix GeneChip probe level data
-
Irizarry, R. A., Bolstad, B. M., Collin, F., Cope, L. M., Hobbs, B., and Speed, T. P. (2003). Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Research 31, e15.
-
(2003)
Nucleic Acids Research
, vol.31
-
-
Irizarry, R.A.1
Bolstad, B.M.2
Collin, F.3
Cope, L.M.4
Hobbs, B.5
Speed, T.P.6
-
20
-
-
0141792846
-
Expression of replication-licensing factors MCM2 and MCM3 in normal, hyperplastic, and carcinomatous endometrium: Correlation with expression of Ki-67 and estrogen and progesterone receptors
-
Kato, K., Toki, T., Shimizu, M., Shiozawa, T., Fujii, S., Nakaido, T., and Konishi, I. (2003). Expression of replication-licensing factors MCM2 and MCM3 in normal, hyperplastic, and carcinomatous endometrium: Correlation with expression of Ki-67 and estrogen and progesterone receptors. Internation Journal of Gynecological Pathology 22, 334-340.
-
(2003)
Internation Journal of Gynecological Pathology
, vol.22
, pp. 334-340
-
-
Kato, K.1
Toki, T.2
Shimizu, M.3
Shiozawa, T.4
Fujii, S.5
Nakaido, T.6
Konishi, I.7
-
21
-
-
43149125186
-
A gene expression network model of type 2 diabetes links cell cycle regulation in islets with diabetes susceptibility
-
Keller, M. P., Choi, Y., Wang, P., Davis, D. B., Rabaglia, M. E., Oler, A. T., Stapleton, D. S., Argmann, C., Schueler, K. L., Edwards, S., Steinberg, H. A., Neto, E. C., Kleinhanz, R., Turner, S., Hellerstein, M. K., Shadt, E. E., Yandell, B. S., Kendziorski, C., and Attie, A. D. (2008). A gene expression network model of type 2 diabetes links cell cycle regulation in islets with diabetes susceptibility. Genome Research 18, 706-716.
-
(2008)
Genome Research
, vol.18
, pp. 706-716
-
-
Keller, M.P.1
Choi, Y.2
Wang, P.3
Davis, D.B.4
Rabaglia, M.E.5
Oler, A.T.6
Stapleton, D.S.7
Argmann, C.8
Schueler, K.L.9
Edwards, S.10
Steinberg, H.A.11
Neto, E.C.12
Kleinhanz, R.13
Turner, S.14
Hellerstein, M.K.15
Shadt, E.E.16
Yandell, B.S.17
Kendziorski, C.18
Attie, A.D.19
-
22
-
-
0346888587
-
On parametric empirical Bayes methods for comparing multiple groups using replicated gene expression profiles
-
Kendziorski, C. M., Newton, M. A., Lan, H., and Gould, M. N. (2003). On parametric empirical Bayes methods for comparing multiple groups using replicated gene expression profiles. Statistics in Medicine 22, 3899-3914.
-
(2003)
Statistics in Medicine
, vol.22
, pp. 3899-3914
-
-
Kendziorski, C.M.1
Newton, M.A.2
Lan, H.3
Gould, M.N.4
-
23
-
-
10244219943
-
A statistical method for identifying differential gene-gene co-expression patterns
-
Lai, Y., Wu, B., Chen, L., and Zhao, H. (2004). A statistical method for identifying differential gene-gene co-expression patterns. Bioinformatics 20, 3146-3155.
-
(2004)
Bioinformatics
, vol.20
, pp. 3146-3155
-
-
Lai, Y.1
Wu, B.2
Chen, L.3
Zhao, H.4
-
24
-
-
0035629944
-
Is the property of being positively correlated transitive?
-
Langford, E., Schwertman, N., and Owens, M. (2001). Is the property of being positively correlated transitive? The American Statistician 55, 322-325.
-
(2001)
The American Statistician
, vol.55
, pp. 322-325
-
-
Langford, E.1
Schwertman, N.2
Owens, M.3
-
25
-
-
0037168518
-
Genome-wide coexpression dynamics: Theory and application
-
Li, K.-C. (2002). Genome-wide coexpression dynamics: Theory and application. PNAS 99, 16875-16880.
-
(2002)
PNAS
, vol.99
, pp. 16875-16880
-
-
Li, K.-C.1
-
28
-
-
74049143935
-
Dissecting the dynamics of dysregulation of cellular processes in mouse mammary glad tumor
-
Mentzen, W. I., Floris, M., and de la Fuente, A. (2009). Dissecting the dynamics of dysregulation of cellular processes in mouse mammary glad tumor. BMC Genomics 10, 601.
-
(2009)
BMC Genomics
, vol.10
, pp. 601
-
-
Mentzen, W.I.1
Floris, M.2
de la Fuente, A.3
-
29
-
-
34250305651
-
Random-set methods identify distinct aspects of the enrichment signal in gene-set analysis
-
Newton, M. A., Quintana, F. A., den Boon, J. A., Sengupta, S., and Ahlquist, P. (2007). Random-set methods identify distinct aspects of the enrichment signal in gene-set analysis. The Annals of Applied Statistics 1, 85-106.
-
(2007)
The Annals of Applied Statistics
, vol.1
, pp. 85-106
-
-
Newton, M.A.1
Quintana, F.A.2
den Boon, J.A.3
Sengupta, S.4
Ahlquist, P.5
-
30
-
-
34548329530
-
A perspective on dna microarrays in pathology research and practice
-
Pollack, J. R. (2007). A perspective on dna microarrays in pathology research and practice. American Journal of Pathology 171, 375-385.
-
(2007)
American Journal of Pathology
, vol.171
, pp. 375-385
-
-
Pollack, J.R.1
-
31
-
-
77952487199
-
-
Technical Report NA06, DAMTP, University of Cambridge, Cambridge, UK.
-
Powell, M. J. D. (2009). The BOBYQA algorithm for bound constrained optimization without Derivatives. Technical Report NA06, DAMTP, University of Cambridge, Cambridge, UK
-
(2009)
The BOBYQA algorithm for bound constrained optimization without Derivatives
-
-
Powell, M.J.D.1
-
32
-
-
25444485444
-
The effects of normalization on the correlation structure of microarray data
-
Qiu, X., Brooks, A. I., Klebanov, L., and Yakovlev, A. (2005). The effects of normalization on the correlation structure of microarray data. BMC Bioinformatics 6, 120.
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 120
-
-
Qiu, X.1
Brooks, A.I.2
Klebanov, L.3
Yakovlev, A.4
-
33
-
-
84863304598
-
-
R Development Core Team. Vienna, Austria : R Foundation for Statistical Computing. Available at: Accessed August 11, 2011.
-
R Development Core Team. (2009). R: A Language and Environment for Statistical Computing. Vienna, Austria : R Foundation for Statistical Computing. Available at: Accessed August 11, 2011.
-
(2009)
R: A Language and Environment for Statistical Computing
-
-
-
34
-
-
33644872577
-
Limma: Linear models for microarray data
-
R. Gentleman, V. Carey, S. Dudoit, R. Irizarry, and W. Huber (eds), New York : Springer.
-
Smyth, G. K. (2005). Limma: Linear models for microarray data. In Bioinformatics and Computational Biology Solutions using R and Bioconductor, R. Gentleman, V. Carey, S. Dudoit, R. Irizarry, and W. Huber (eds), 397-420. New York : Springer.
-
(2005)
Bioinformatics and Computational Biology Solutions using R and Bioconductor
, pp. 397-420
-
-
Smyth, G.K.1
-
36
-
-
27344435774
-
Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles
-
Subramanian, A., Tamayo, P., Mootha, V. K., Mukherjee, A., Ebert, B. L., Gillette, M. A., Paulovich, A., Pomeroy, S. L., Golub, T. R., Lander, E. S., and Mesirov, J. P. (2005). Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. PNAS 102, 15545-15550.
-
(2005)
PNAS
, vol.102
, pp. 15545-15550
-
-
Subramanian, A.1
Tamayo, P.2
Mootha, V.K.3
Mukherjee, A.4
Ebert, B.L.5
Gillette, M.A.6
Paulovich, A.7
Pomeroy, S.L.8
Golub, T.R.9
Lander, E.S.10
Mesirov, J.P.11
-
37
-
-
0031880105
-
Isolation of a novel tp53 target gene from a colon cancer cell line carrying a highly regulated wild-type tp53
-
Takei, Y., Ishikawa, S., Tokino, T., Muto, T., and Nakamura, Y. (1998). Isolation of a novel tp53 target gene from a colon cancer cell line carrying a highly regulated wild-type tp53. Genes, Chromosomes and Cancer 23, 1-9.
-
(1998)
Genes, Chromosomes and Cancer
, vol.23
, pp. 1-9
-
-
Takei, Y.1
Ishikawa, S.2
Tokino, T.3
Muto, T.4
Nakamura, Y.5
-
38
-
-
85153153034
-
-
The Human Gene Compendium. prostate androgen-regulated mucin-like protein 1. Available at: Accessed August 11, 2011.
-
The Human Gene Compendium. (2011). prostate androgen-regulated mucin-like protein 1. Available at: Accessed August 11, 2011.
-
(2011)
-
-
-
39
-
-
34547649056
-
Coxpress: Differential co-expression in gene expression data
-
Watson, M. (2006). Coxpress: Differential co-expression in gene expression data. BMC Bioinformatics 7, 509.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 509
-
-
Watson, M.1
-
42
-
-
35748952199
-
A gene expression bar code for microarray data
-
Zilliox, M. J. and Irizarry, R. A. (2007). A gene expression bar code for microarray data. Nature Methods 4, 911-913.
-
(2007)
Nature Methods
, vol.4
, pp. 911-913
-
-
Zilliox, M.J.1
Irizarry, R.A.2
|