-
1
-
-
34249663294
-
Analyzing gene expression data in terms of gene sets: Methodological issues
-
DOI 10.1093/bioinformatics/btm051
-
Goeman, J.J. and Bü hlmann, P. (2007) Analyzing gene expression data in terms of gene sets: methodological issues. Bioinformatics, 23, 980-987. (Pubitemid 47050585)
-
(2007)
Bioinformatics
, vol.23
, Issue.8
, pp. 980-987
-
-
Goeman, J.J.1
Buhlmann, P.2
-
2
-
-
26444608611
-
Discovering statistically significant pathways in expression profiling studies
-
DOI 10.1073/pnas.0506577102
-
Tian, L., Greenberg, S.A., Kong, S.W., Altschuler, J., Kohane, I.S. and Park, P.J. (2005) Discovering statistically significant pathways in expression profiling studies. Proc. Natl Acad. Sci. U.S.A, 102, 13544-13549. (Pubitemid 41420885)
-
(2005)
Proceedings of the National Academy of Sciences of the United States of America
, vol.102
, Issue.38
, pp. 13544-13549
-
-
Tian, L.1
Greenberg, S.A.2
Kong, S.W.3
Altschuler, J.4
Kohane, I.S.5
Park, P.J.6
-
3
-
-
0345832338
-
A global test for groups fo genes: Testing association with a clinical outcome
-
DOI 10.1093/bioinformatics/btg382
-
Goeman, J.J., van de Geer, S.A., de Kort, F. and van Houwelingen, H.C. (2004) A global test for groups of genes: testing association with a clinical outcome. Bioinformatics, 20, 93-99. (Pubitemid 38088346)
-
(2004)
Bioinformatics
, vol.20
, Issue.1
, pp. 93-99
-
-
Goeman, J.J.1
Van De Geer, S.2
De Kort, F.3
Van Houwellingen, H.C.4
-
4
-
-
33845902772
-
Absolute enrichment: Gene set enrichment analysis for homeostatic systems
-
Saxena, V., Orgill, D. and Kohane, I. (2006) Absolute enrichment: gene set enrichment analysis for homeostatic systems. Nucleic Acids Res., 34, e151.
-
(2006)
Nucleic Acids Res.
, vol.34
-
-
Saxena, V.1
Orgill, D.2
Kohane, I.3
-
5
-
-
34547483895
-
Improving gene set analysis of microarray data by SAM-GS
-
Dinu, I., Potter, J.D., Mueller, T., Liu, Q., Adewale, A.J., Jhangri, G.S., Einecke, G., Famulski, K.S., Halloran, P. and Yasui, Y. (2007) Improving gene set analysis of microarray data by SAM-GS. BMC Bioinformatics, 8, 242.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 242
-
-
Dinu, I.1
Potter, J.D.2
Mueller, T.3
Liu, Q.4
Adewale, A.J.5
Jhangri, G.S.6
Einecke, G.7
Famulski, K.S.8
Halloran, P.9
Yasui, Y.10
-
6
-
-
33847324900
-
Extensions to gene set enrichment
-
DOI 10.1093/bioinformatics/btl599
-
Jiang, Z. and Gentleman, R. (2007) Extensions to gene set enrichment. Bioinformatics, 23, 306-313. (Pubitemid 46323152)
-
(2007)
Bioinformatics
, vol.23
, Issue.3
, pp. 306-313
-
-
Jiang, Z.1
Gentleman, R.2
-
7
-
-
55749111082
-
Gene set enrichment analysis using linear models and diagnostics
-
Oron, A.P., Jiang, Z. and Gentleman, R. (2008) Gene set enrichment analysis using linear models and diagnostics. Bioinformatics, 24, 2586-2591.
-
(2008)
Bioinformatics
, vol.24
, pp. 2586-2591
-
-
Oron, A.P.1
Jiang, Z.2
Gentleman, R.3
-
8
-
-
77955889132
-
ROAST: Rotation gene set tests for complex microarray experiments
-
Wu, D., Lim, E., Vaillant, F., Asselin-Labat, M.L., Visvader, J.E. and Smyth, G.K. (2010) ROAST: rotation gene set tests for complex microarray experiments. Bioinformatics, 26, 2176-2182.
-
(2010)
Bioinformatics
, vol.26
, pp. 2176-2182
-
-
Wu, D.1
Lim, E.2
Vaillant, F.3
Asselin-Labat, M.L.4
Visvader, J.E.5
Smyth, G.K.6
-
9
-
-
77957889565
-
Heading down the wrong pathway: On the influence of correlation within gene sets
-
Gatti, D.M., Barry, W.T., Nobel, A.B., Rusyn, I. and Wright, F.A. (2010) Heading down the wrong pathway: on the influence of correlation within gene sets. BMC Genomics, 11, 574.
-
(2010)
BMC Genomics
, vol.11
, pp. 574
-
-
Gatti, D.M.1
Barry, W.T.2
Nobel, A.B.3
Rusyn, I.4
Wright, F.A.5
-
10
-
-
13244279520
-
Comparing functional annotation analyses with Catmap
-
Breslin, T., Edén, P. and Krogh, M. (2004) Comparing functional annotation analyses with Catmap. BMC Bioinformatics, 5, 193.
-
(2004)
BMC Bioinformatics
, vol.5
, pp. 193
-
-
Breslin, T.1
Edén, P.2
Krogh, M.3
-
11
-
-
3242886987
-
GOAL: Automated Gene Ontology analysis of expression profiles
-
DOI 10.1093/nar/gkh443
-
Volinia, S., Evangelisti, R., Francioso, F., Arcelli, D., Carella, M. and Gasparini, P. (2004) GOAL: automated Gene Ontology analysis of expression profiles. Nucleic Acids Res., 32, W492-W499. (Pubitemid 38997382)
-
(2004)
Nucleic Acids Research
, vol.32
, Issue.WEB SERVER ISS.
-
-
Volinia, S.1
Evangelisti, R.2
Francioso, F.3
Arcelli, D.4
Carella, M.5
Gasparini, P.6
-
12
-
-
8844265260
-
GO-Mapper: Functional analysis of gene expression data using the expression level as a score to evaluate Gene Ontology terms
-
DOI 10.1093/bioinformatics/bth293
-
Smid, M. and Dorssers, L.C. (2004) GO-Mapper: functional analysis of gene expression data using the expression level as a score to evaluate Gene Ontology terms. Bioinformatics, 20, 2618-2625. (Pubitemid 39530148)
-
(2004)
Bioinformatics
, vol.20
, Issue.16
, pp. 2618-2625
-
-
Smid, M.1
Dorssers, L.C.J.2
-
13
-
-
25444502609
-
PAGE: Parametric analysis of gene set enrichment
-
Kim, S.Y. and Volsky, D.J. (2005) PAGE: parametric analysis of gene set enrichment. BMC Bioinformatics, 6, 144.
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 144
-
-
Kim, S.Y.1
Volsky, D.J.2
-
14
-
-
23144463134
-
T-profiler: Scoring the activity of predefined groups of genes using gene expression data
-
DOI 10.1093/nar/gki484
-
Boorsma, A., Foat, B.C., Vis, D., Klis, F. and Bussemaker, H.J. (2005) T-profiler: scoring the activity of predefined groups of genes using gene expression data. Nucleic Acids Res., 33, W592-W595. (Pubitemid 44529991)
-
(2005)
Nucleic Acids Research
, vol.33
, Issue.WEB. SERV. ISS.
-
-
Boorsma, A.1
Foat, B.C.2
Vis, D.3
Klis, F.4
Bussemaker, H.J.5
-
15
-
-
33748690756
-
ADGO: Analysis of differentially expressed gene sets using composite GO annotation
-
DOI 10.1093/bioinformatics/btl378
-
Nam, D., Kim, S.B., Kim, S.K., Yang, S., Kim, S.Y. and Chu, I.S. (2006) ADGO: analysis of differentially expressed gene sets using composite GO annotation. Bioinformatics, 22, 2249-2253. (Pubitemid 44390880)
-
(2006)
Bioinformatics
, vol.22
, Issue.18
, pp. 2249-2253
-
-
Nam, D.1
Kim, S.-B.2
Kim, S.-K.3
Yang, S.4
Kim, S.-Y.5
Chu, I.-S.6
-
16
-
-
67649202800
-
GAGE: Generally applicable gene set enrichment for pathway analysis
-
(Electronic 1471-2105) (Linking)
-
Luo, W., Friedman, M.S., Shedden, K., Hankenson, K.D. and Woolf, P.J. (2009) GAGE: generally applicable gene set enrichment for pathway analysis. BMC Bioinformatics, 10, 1471-2105, (Electronic) 1471-2105 (Linking).
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 1471-2105
-
-
Luo, W.1
Friedman, M.S.2
Shedden, K.3
Hankenson, K.D.4
Woolf, P.J.5
-
17
-
-
35348890683
-
On testing the significance of sets of genes
-
Efron, B. and Tibshirani, R. (2007) On testing the significance of sets of genes. Ann. Appl. Statist., 1, 107-129.
-
(2007)
Ann. Appl. Statist.
, vol.1
, pp. 107-129
-
-
Efron, B.1
Tibshirani, R.2
-
18
-
-
84869590034
-
Rotation testing in gene set enrichment analysis for small direct comparison experiments
-
Article34
-
Dørum, G., Snipen, L., Solheim, M. and Saebo, S. (2009) Rotation testing in gene set enrichment analysis for small direct comparison experiments. Stat. Appl. Genet. Mol. Biol., 8, Article34.
-
(2009)
Stat. Appl. Genet. Mol. Biol.
, vol.8
-
-
Dørum, G.1
Snipen, L.2
Solheim, M.3
Saebo, S.4
-
19
-
-
18744389489
-
Significance analysis of functional categories in gene expression studies: A structured permutation approach
-
DOI 10.1093/bioinformatics/bti260
-
Barry, W.T., Nobel, A.B. and Wright, F.A. (2005) Significance analysis of functional categories in gene expression studies: a structured permutation approach. Bioinformatics, 21, 1943-1949. (Pubitemid 40668030)
-
(2005)
Bioinformatics
, vol.21
, Issue.9
, pp. 1943-1949
-
-
Barry, W.T.1
Nobel, A.B.2
Wright, F.A.3
-
20
-
-
27344435774
-
Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles
-
DOI 10.1073/pnas.0506580102
-
Subramanian, A., Tamayo, P., Mootha, V.K., Mukherjee, S., Ebert, B.L., Gillette, M.A., Paulovich, A., Pomeroy, S.L., Golub, T.R., Lander, E.S. et al. (2005) Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl Acad. Sci. U.S.A, 102, 15545-15550. (Pubitemid 41528093)
-
(2005)
Proceedings of the National Academy of Sciences of the United States of America
, vol.102
, Issue.43
, pp. 15545-15550
-
-
Subramanian, A.1
Tamayo, P.2
Mootha, V.K.3
Mukherjee, S.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
-
21
-
-
77956524952
-
De-correlating expression in gene-set analysis
-
Nam, D. (2010) De-correlating expression in gene-set analysis. Bioinformatics, 26, i511-i516.
-
(2010)
Bioinformatics
, vol.26
-
-
Nam, D.1
-
22
-
-
48249108773
-
An integrated approach for the analysis of biological pathways using mixed models
-
Wang, L., Zhang, B., Wolfinger, R.D. and Chen, X. (2008) An integrated approach for the analysis of biological pathways using mixed models. PLoS Genet., 4, e1000115.
-
(2008)
PLoS Genet
, vol.4
-
-
Wang, L.1
Zhang, B.2
Wolfinger, R.D.3
Chen, X.4
-
23
-
-
73849140082
-
A unified mixed effects model for gene set analysis of time course microarray experiments
-
8, Article 47
-
Wang, L., Chen, X., Wolfinger, R., Franklin, J., Coffey, R. and Zhang, B. (2009) A unified mixed effects model for gene set analysis of time course microarray experiments. Stat. Appl. Genet. Mol. Biol., 8, Article 47.
-
(2009)
Stat. Appl. Genet. Mol. Biol.
-
-
Wang, L.1
Chen, X.2
Wolfinger, R.3
Franklin, J.4
Coffey, R.5
Zhang, B.6
-
24
-
-
4544341015
-
Linear models and empirical Bayes methods for assessing differential expression in microarray experiments
-
3, Article3
-
Smyth, G.K. (2004) Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Stat. Appl. Genet. Mol. Biol., 3, Article3.
-
(2004)
Stat. Appl. Genet. Mol. Biol.
-
-
Smyth, G.K.1
-
25
-
-
33644872577
-
Limma: Linear models for microarray data
-
Gentleman, R., Carey, V., Dudoit, S., Irizarry, R. and Huber, W. (eds Springer, NY
-
Smyth, G.K. (2005) Limma: linear models for microarray data. In: Gentleman, R., Carey, V., Dudoit, S., Irizarry, R. and Huber, W. (eds), Bioinformatics and Computational Biology Solutions using R and Bioconductor. Springer, NY, pp. 397-420.
-
(2005)
Bioinformatics and Computational Biology Solutions Using R and Bioconductor
, pp. 397-420
-
-
Smyth, G.K.1
-
26
-
-
28744458859
-
Bioconductor: Open software development for computational biology and bioinformatics
-
Gentleman, R., Carey, V., Bates, D., Bolstad, B., Dettling, M., Dudoit, S., Ellis, B., Gautier, L., Ge, Y., Gentry, J. et al. (2004) Bioconductor: open software development for computational biology and bioinformatics. Genome Biol., 5, R80.
-
(2004)
Genome Biol
, vol.5
-
-
Gentleman, R.1
Carey, V.2
Bates, D.3
Bolstad, B.4
Dettling, M.5
Dudoit, S.6
Ellis, B.7
Gautier, L.8
Ge, Y.9
Gentry, J.10
-
27
-
-
51249106466
-
Integrative analysis of RUNX1 downstream pathways and target genes
-
Michaud, J., Simpson, K., Escher, R., Buchet-Poyau, K., Beissbarth, T., Carmichael, C., Ritchie, M., Schutz, F., Cannon, P., Liu, M. et al. (2008) Integrative analysis of RUNX1 downstream pathways and target genes. BMC Genomics, 9, 363.
-
(2008)
BMC Genomics
, vol.9
, pp. 363
-
-
Michaud, J.1
Simpson, K.2
Escher, R.3
Buchet-Poyau, K.4
Beissbarth, T.5
Carmichael, C.6
Ritchie, M.7
Schutz, F.8
Cannon, P.9
Liu, M.10
-
28
-
-
0004252445
-
-
4th edn Pentice-Hall International, Upper Saddle River, New Jersey
-
Zar, J. (1999) Biostatistical Analysis, 4th edn. Pentice-Hall International, Upper Saddle River, New Jersey.
-
(1999)
Biostatistical Analysis
-
-
Zar, J.1
-
29
-
-
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. Ann. Appl. Stat., 2, 286-315.
-
(2008)
Ann. Appl. Stat.
, vol.2
, pp. 286-315
-
-
Barry, W.T.1
Nobel, A.B.2
Wright, F.A.3
-
30
-
-
34548863946
-
Identification of conserved gene expression features between murine mammary carcinoma models and human breast tumors
-
Herschkowitz, J.I., Simin, K., Weigman, V.J., Mikaelian, I., Usary, J., Hu, Z., Rasmussen, K.E., Jones, L.P., Assefnia, S., Chandrasekharan, S. et al. (2007) Identification of conserved gene expression features between murine mammary carcinoma models and human breast tumors. Genome Bio., 8, R76.
-
(2007)
Genome Bio
, vol.8
-
-
Herschkowitz, J.I.1
Simin, K.2
Weigman, V.J.3
Mikaelian, I.4
Usary, J.5
Hu, Z.6
Rasmussen, K.E.7
Jones, L.P.8
Assefnia, S.9
Chandrasekharan, S.10
-
31
-
-
68349130357
-
Aberrant luminal progenitors as the candidate target population for basal tumor development in BRCA1 mutation carriers
-
Lim, E., Vaillant, F., Wu, D., Forrest, N.C., Pal, B., Hart, A.H., Asselin-Labat, M.L., Gyorki, D.E., Ward, T., Partanen, A. et al. (2009) Aberrant luminal progenitors as the candidate target population for basal tumor development in BRCA1 mutation carriers. Nat. Med., 15, 907-913.
-
(2009)
Nat. Med.
, vol.15
, pp. 907-913
-
-
Lim, E.1
Vaillant, F.2
Wu, D.3
Forrest, N.C.4
Pal, B.5
Hart, A.H.6
Asselin-Labat, M.L.7
Gyorki, D.E.8
Ward, T.9
Partanen, A.10
-
32
-
-
78650483491
-
Optimizing the noise versus bias trade-off for Illumina Whole Genome Expression BeadChips
-
Shi, W., Oshlack, A. and Smyth, G. (2010) Optimizing the noise versus bias trade-off for Illumina Whole Genome Expression BeadChips. Nucleic Acids Res., 38, e204.
-
(2010)
Nucleic Acids Res.
, vol.38
-
-
Shi, W.1
Oshlack, A.2
Smyth, G.3
-
33
-
-
78149276744
-
Permutation p-values should never be zero: Calculating exact p-values when permutations are randomly drawn
-
Article 39
-
Phipson, B. and Smyth, G. (2010) Permutation p-values should never be zero: calculating exact p-values when permutations are randomly drawn. Stat. Appl. Genet. Mol. Biol., 9, Article 39.
-
(2010)
Stat. Appl. Genet. Mol. Biol.
, vol.9
-
-
Phipson, B.1
Smyth, G.2
-
34
-
-
84913393586
-
Effect of dependence on the level of some one-sample tests
-
Gastwirth, J.L. and Rubin, H. (1971) Effect of dependence on the level of some one-sample tests. J. Am. Stat. Assoc., 66, 816-820.
-
(1971)
J. Am. Stat. Assoc.
, vol.66
, pp. 816-820
-
-
Gastwirth, J.L.1
Rubin, H.2
-
35
-
-
79958135926
-
Molecular signatures database (MSigDB) 3.0
-
Liberzon, A., Subramanian, A., Pinchback, R., Thorvaldsdó ttir, H., Tamayo, P. and Mesirov, J. (2011) Molecular signatures database (MSigDB) 3.0. Bioinformatics, 27, 1739-1740.
-
(2011)
Bioinformatics
, vol.27
, pp. 1739-1740
-
-
Liberzon, A.1
Subramanian, A.2
Pinchback, R.3
Thorvaldsdóttir, H.4
Tamayo, P.5
Mesirov, J.6
-
36
-
-
42649112047
-
An embryonic stem cell-like gene expression signature in poorly differentiated aggressive human tumors
-
DOI 10.1038/ng.127, PII NG127
-
Ben-Porath, I., Thomson, M., Carey, V., Ge, R., Bell, G., Regev, A. and Weinberg, R. (2008) An embryonic stem cell-like gene expression signature in poorly differentiated aggressive human tumors. Nat. Genet., 40, 499-507. (Pubitemid 351601215)
-
(2008)
Nature Genetics
, vol.40
, Issue.5
, pp. 499-507
-
-
Ben-Porath, I.1
Thomson, M.W.2
Carey, V.J.3
Ge, R.4
Bell, G.W.5
Regev, A.6
Weinberg, R.A.7
-
37
-
-
84863012487
-
A mammary stem cell population identified and characterized in late embryogenesis reveals similarities to human breast cancer
-
Spike, B., Engle, D., Lin, J., Cheung, S., La, J. and Wahl, G. (2012) A mammary stem cell population identified and characterized in late embryogenesis reveals similarities to human breast cancer. Cell Stem Cell, 10, 183-197.
-
(2012)
Cell Stem Cell
, vol.10
, pp. 183-197
-
-
Spike, B.1
Engle, D.2
Lin, J.3
Cheung La S, J.4
Wahl, G.5
-
38
-
-
77956218241
-
BRCA1 basal-like breast cancers originate from luminal epithelial progenitors and not from basal stem cells
-
Molyneux, G., Geyer, F., Magnay, F., McCarthy, A., Kendrick, H., Natrajan, R., Mackay, A., Grigoriadis, A., Tutt, A., Ashworth, A. et al. (2010) BRCA1 basal-like breast cancers originate from luminal epithelial progenitors and not from basal stem cells. Cell Stem Cell, 7, 403-417.
-
(2010)
Cell Stem Cell
, vol.7
, pp. 403-417
-
-
Molyneux, G.1
Geyer, F.2
Magnay, F.3
McCarthy, A.4
Kendrick, H.5
Natrajan, R.6
MacKay, A.7
Grigoriadis, A.8
Tutt, A.9
Ashworth, A.10
|