-
1
-
-
81555216077
-
Gene expression profiling in breast cancer: Classification, prognostication, and prediction
-
Reis-Filho, J. S., Pusztai, L. Gene expression profiling in breast cancer: classification, prognostication, and prediction. Lancet 378, 1812-1823 (2011).
-
(2011)
Lancet
, vol.378
, pp. 1812-1823
-
-
Reis-Filho, J.S.1
Pusztai, L.2
-
2
-
-
0034680102
-
Molecular portraits of human breast tumours
-
Perou, C. M. et al. Molecular portraits of human breast tumours. Nature 406, 747-752 (2000).
-
(2000)
Nature
, vol.406
, pp. 747-752
-
-
Perou, C.M.1
-
3
-
-
0037478605
-
Repeated observation of breast tumour subtypes in independent gene expression data sets
-
Sorlie, T. et al. Repeated observation of breast tumour subtypes in independent gene expression data sets. Proc. Natl Acad. Sci. USA 100, 8418-8423 (2003).
-
(2003)
Proc. Natl Acad. Sci. USA
, vol.100
, pp. 8418-8423
-
-
Sorlie, T.1
-
4
-
-
84877028141
-
Comprehensive molecular portraits of human breast tumours
-
TCGA
-
TCGA. Comprehensive molecular portraits of human breast tumours. Nature 490, 61-70 (2012).
-
(2012)
Nature
, vol.490
, pp. 61-70
-
-
-
5
-
-
84861527388
-
The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups
-
Curtis, C. et al. The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups. Nature 486, 346-352 (2012).
-
(2012)
Nature
, vol.486
, pp. 346-352
-
-
Curtis, C.1
-
6
-
-
78049443323
-
Proteomic changes resulting from gene copy number variations in cancer cells
-
Geiger, T., Cox, J., Mann, M. Proteomic changes resulting from gene copy number variations in cancer cells. PLoS Genet. 6, e1001090 (2010).
-
(2010)
PLoS Genet.
, vol.6
, pp. e1001090
-
-
Geiger, T.1
Cox, J.2
Mann, M.3
-
7
-
-
84907269780
-
Proteogenomic characterization of human colon and rectal cancer
-
Zhang, B. et al. Proteogenomic characterization of human colon and rectal cancer. Nature 513, 382-387 (2014).
-
(2014)
Nature
, vol.513
, pp. 382-387
-
-
Zhang, B.1
-
8
-
-
80855128254
-
Deep proteome and transcriptome mapping of a human cancer cell line
-
Nagaraj, N. et al. Deep proteome and transcriptome mapping of a human cancer cell line. Mol. Syst. Biol. 7, 548 (2011).
-
(2011)
Mol. Syst. Biol.
, vol.7
, pp. 548
-
-
Nagaraj, N.1
-
9
-
-
79956322553
-
Global quantification of mammalian gene expression control
-
Schwanhausser, B. et al. Global quantification of mammalian gene expression control. Nature 473, 337-342 (2011).
-
(2011)
Nature
, vol.473
, pp. 337-342
-
-
Schwanhausser, B.1
-
10
-
-
84874232489
-
The coming age of complete, accurate, and ubiquitous proteomes
-
Mann, M., Kulak, N. A., Nagaraj, N., Cox, J. The coming age of complete, accurate, and ubiquitous proteomes. Mol. Cell 49, 583-590 (2013).
-
(2013)
Mol. Cell
, vol.49
, pp. 583-590
-
-
Mann, M.1
Kulak, N.A.2
Nagaraj, N.3
Cox, J.4
-
11
-
-
0036583926
-
Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics
-
Ong, S. E. et al. Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol. Cell. Proteomics 1, 376-386 (2002).
-
(2002)
Mol. Cell. Proteomics
, vol.1
, pp. 376-386
-
-
Ong, S.E.1
-
12
-
-
77952226764
-
Super-SILAC mix for quantitative proteomics of human tumour tissue
-
Geiger, T., Cox, J., Ostasiewicz, P., Wisniewski, J. R., Mann, M. Super-SILAC mix for quantitative proteomics of human tumour tissue. Nat. Methods 7, 383-385 (2010).
-
(2010)
Nat. Methods
, vol.7
, pp. 383-385
-
-
Geiger, T.1
Cox, J.2
Ostasiewicz, P.3
Wisniewski, J.R.4
Mann, M.5
-
13
-
-
77954378942
-
Proteome phosphoproteome, and N-glycoproteome are quantitatively preserved in formalin-fixed paraffin-embedded tissue and analyzable by high-resolution mass spectrometry
-
Ostasiewicz, P., Zielinska, D. F., Mann, M., Wisniewski, J. R. Proteome, phosphoproteome, and N-glycoproteome are quantitatively preserved in formalin-fixed paraffin-embedded tissue and analyzable by high-resolution mass spectrometry. J. Proteome Res. 9, 3688-3700 (2010).
-
(2010)
J. Proteome Res.
, vol.9
, pp. 3688-3700
-
-
Ostasiewicz, P.1
Zielinska, D.F.2
Mann, M.3
Wisniewski, J.R.4
-
14
-
-
67349266694
-
Universal sample preparation method for proteome analysis
-
Wisniewski, J. R., Zougman, A., Nagaraj, N., Mann, M. Universal sample preparation method for proteome analysis. Nat. Methods 6, 359-362 (2009).
-
(2009)
Nat. Methods
, vol.6
, pp. 359-362
-
-
Wisniewski, J.R.1
Zougman, A.2
Nagaraj, N.3
Mann, M.4
-
15
-
-
71549117585
-
Combination of FASP and StageTip-based fractionation allows in-depth analysis of the hippocampal membrane proteome
-
Wisniewski, J. R., Zougman, A., Mann, M. Combination of FASP and StageTip-based fractionation allows in-depth analysis of the hippocampal membrane proteome. J. Proteome Res. 8, 5674-5678 (2009).
-
(2009)
J. Proteome Res.
, vol.8
, pp. 5674-5678
-
-
Wisniewski, J.R.1
Zougman, A.2
Mann, M.3
-
16
-
-
80052769923
-
Mass spectrometry-based proteomics using Q Exactive, a high-performance benchtop quadrupole Orbitrap mass spectrometer
-
Michalski, A. et al. Mass spectrometry-based proteomics using Q Exactive, a high-performance benchtop quadrupole Orbitrap mass spectrometer. Mol. Cell. Proteomics 10, M111-011015 (2011).
-
(2011)
Mol. Cell. Proteomics
, vol.10
, pp. M111-011015
-
-
Michalski, A.1
-
17
-
-
57449099865
-
MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification
-
Cox, J., Mann, M. MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat. Biotechnol. 26, 1367-1372 (2008).
-
(2008)
Nat. Biotechnol.
, vol.26
, pp. 1367-1372
-
-
Cox, J.1
Mann, M.2
-
18
-
-
27344435774
-
Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles
-
Subramanian, A. et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl Acad. Sci. USA 102, 15545-15550 (2005).
-
(2005)
Proc. Natl Acad. Sci. USA
, vol.102
, pp. 15545-15550
-
-
Subramanian, A.1
-
19
-
-
33745603978
-
An estrogen receptor-negative breast cancer subset characterized by a hormonally regulated transcriptional program and response to androgen
-
Doane, A. S. et al. An estrogen receptor-negative breast cancer subset characterized by a hormonally regulated transcriptional program and response to androgen. Oncogene 25, 3994-4008 (2006).
-
(2006)
Oncogene
, vol.25
, pp. 3994-4008
-
-
Doane, A.S.1
-
20
-
-
33644778549
-
Laser microdissection and microarray analysis of breast tumours reveal ER-alpha related genes and pathways
-
Yang, F. et al. Laser microdissection and microarray analysis of breast tumours reveal ER-alpha related genes and pathways. Oncogene 25, 1413-1419 (2006).
-
(2006)
Oncogene
, vol.25
, pp. 1413-1419
-
-
Yang, F.1
-
21
-
-
44849114353
-
Subtypes of breast cancer show preferential site of relapse
-
Smid, M. et al. Subtypes of breast cancer show preferential site of relapse. Cancer Res. 68, 3108-3114 (2008).
-
(2008)
Cancer Res.
, vol.68
, pp. 3108-3114
-
-
Smid, M.1
-
22
-
-
34047158128
-
Interferon regulatory factor-1 regulates reconstituted extracellular matrix (rECM)-mediated apoptosis in human mammary epithelial cells
-
Bowie, M. L. et al. Interferon regulatory factor-1 regulates reconstituted extracellular matrix (rECM)-mediated apoptosis in human mammary epithelial cells. Oncogene 26, 2017-2026 (2007).
-
(2007)
Oncogene
, vol.26
, pp. 2017-2026
-
-
Bowie, M.L.1
-
23
-
-
22744448864
-
Identification of molecular apocrine breast tumours by microarray analysis
-
Farmer, P. et al. Identification of molecular apocrine breast tumours by microarray analysis. Oncogene 24, 4660-4671 (2005).
-
(2005)
Oncogene
, vol.24
, pp. 4660-4671
-
-
Farmer, P.1
-
24
-
-
0036092049
-
Transcriptional profiling of interferon regulatory factor 3 target genes: Direct involvement in the regulation of interferon-stimulated genes
-
Grandvaux, N. et al. Transcriptional profiling of interferon regulatory factor 3 target genes: direct involvement in the regulation of interferon-stimulated genes. J. Virol. 76, 5532-5539 (2002).
-
(2002)
J. Virol.
, vol.76
, pp. 5532-5539
-
-
Grandvaux, N.1
-
25
-
-
35948958955
-
TLR4 enhances TGF-beta signaling and hepatic fibrosis
-
Seki, E. et al. TLR4 enhances TGF-beta signaling and hepatic fibrosis. Nat. Med. 13, 1324-1332 (2007).
-
(2007)
Nat. Med.
, vol.13
, pp. 1324-1332
-
-
Seki, E.1
-
26
-
-
51349088017
-
Biological processes associated with breast cancer clinical outcome depend on the molecular subtypes
-
Desmedt, C. et al. Biological processes associated with breast cancer clinical outcome depend on the molecular subtypes. Clin. Cancer Res. 14, 5158-5165 (2008).
-
(2008)
Clin. Cancer Res.
, vol.14
, pp. 5158-5165
-
-
Desmedt, C.1
-
27
-
-
62449131093
-
Supervised risk predictor of breast cancer based on intrinsic subtypes
-
Parker, J. S. et al. Supervised risk predictor of breast cancer based on intrinsic subtypes. J. Clin. Oncol. 27, 1160-1167 (2009).
-
(2009)
J. Clin. Oncol.
, vol.27
, pp. 1160-1167
-
-
Parker, J.S.1
-
28
-
-
37549020704
-
Recurrent gross mutations of the PTEN tumour suppressor gene in breast cancers with deficient DSB repair
-
Saal, L. H. et al. Recurrent gross mutations of the PTEN tumour suppressor gene in breast cancers with deficient DSB repair. Nat. Genet. 40, 102-107 (2008).
-
(2008)
Nat. Genet.
, vol.40
, pp. 102-107
-
-
Saal, L.H.1
-
29
-
-
78651250284
-
FOXA1 is a key determinant of estrogen receptor function and endocrine response
-
Hurtado, A., Holmes, K. A., Ross-Innes, C. S., Schmidt, D., Carroll, J. S. FOXA1 is a key determinant of estrogen receptor function and endocrine response. Nat. Genet. 43, 27-33 (2011).
-
(2011)
Nat. Genet.
, vol.43
, pp. 27-33
-
-
Hurtado, A.1
Holmes, K.A.2
Ross-Innes, C.S.3
Schmidt, D.4
Carroll, J.S.5
-
30
-
-
84953327329
-
-
ACM Press, Pittsburgh, PA, USA
-
Boser, B. E., Guyon, I. M., Vapnik, V. N. in Proceedings of the 5th Annual Workshop on Computational Learning Theory COLT'92 (ACM Press, Pittsburgh, PA, USA, 1992).
-
(1992)
Proceedings of the 5th Annual Workshop on Computational Learning Theory COLT'92
-
-
Boser, B.E.1
Guyon, I.M.2
Vapnik, V.N.3
-
32
-
-
80051923932
-
Functional genomics reveal that the serine synthesis pathway is essential in breast cancer
-
Possemato, R. et al. Functional genomics reveal that the serine synthesis pathway is essential in breast cancer. Nature 476, 346-350 (2011).
-
(2011)
Nature
, vol.476
, pp. 346-350
-
-
Possemato, R.1
-
33
-
-
84876434755
-
Loss of FBP1 by Snail-mediated repression provides metabolic advantages in basal-like breast cancer
-
Dong, C. et al. Loss of FBP1 by Snail-mediated repression provides metabolic advantages in basal-like breast cancer. Cancer Cell 23, 316-331 (2013).
-
(2013)
Cancer Cell
, vol.23
, pp. 316-331
-
-
Dong, C.1
-
34
-
-
42649112047
-
An embryonic stem cell-like gene expression signature in poorly differentiated aggressive human tumours
-
Ben-Porath, I. et al. An embryonic stem cell-like gene expression signature in poorly differentiated aggressive human tumours. Nat. Genet. 40, 499-507 (2008).
-
(2008)
Nat. Genet.
, vol.40
, pp. 499-507
-
-
Ben-Porath, I.1
-
35
-
-
18244409687
-
Gene expression profiling predicts clinical outcome of breast cancer
-
van 't Veer, L. J. et al. Gene expression profiling predicts clinical outcome of breast cancer. Nature 415, 530-536 (2002).
-
(2002)
Nature
, vol.415
, pp. 530-536
-
-
An 'T Veer, L.J.1
-
36
-
-
84867527044
-
Metabolic associations of reduced proliferation and oxidative stress in advanced breast cancer
-
Jerby, L. et al. Metabolic associations of reduced proliferation and oxidative stress in advanced breast cancer. Cancer Res. 72, 5712-5720 (2012).
-
(2012)
Cancer Res.
, vol.72
, pp. 5712-5720
-
-
Jerby, L.1
-
37
-
-
84921350759
-
PTEN deficiency and mutant p53 confer glucose-addiction to thyroid cancer cells: Impact of glucose depletion on cell proliferation, cell survival, autophagy and cell migration
-
Morani, F. et al. PTEN deficiency and mutant p53 confer glucose-addiction to thyroid cancer cells: impact of glucose depletion on cell proliferation, cell survival, autophagy and cell migration. Genes Cancer 5, 226-239 (2014).
-
(2014)
Genes Cancer
, vol.5
, pp. 226-239
-
-
Morani, F.1
-
38
-
-
79953701087
-
Andromeda: A Peptide Search Engine Integrated into the MaxQuant Environment
-
Cox, J. et al. Andromeda: A Peptide Search Engine Integrated into the MaxQuant Environment. J. Proteome Res. 10, 1794-1805 (2011).
-
(2011)
J. Proteome Res.
, vol.10
, pp. 1794-1805
-
-
Cox, J.1
-
39
-
-
84863304598
-
-
R Core Team R Foundation for Statistical Computing Vienna Austria Available at
-
R Core Team. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria (2012). Available at www.R-project.org/.
-
(2012)
R: A Language and Environment for Statistical Computing
-
-
-
40
-
-
84873508256
-
1D and 2D annotation enrichment: A statistical method integrating quantitative proteomics with complementary high-throughput data
-
Cox, J., Mann, M. 1D and 2D annotation enrichment: a statistical method integrating quantitative proteomics with complementary high-throughput data. BMC Bioinform. 13 (Suppl 16): S12 (2012).
-
(2012)
BMC Bioinform.
, vol.13
, pp. S12
-
-
Cox, J.1
Mann, M.2
-
41
-
-
0001677717
-
Controlling the false discovery rate: A practical and powerful approach to multiple testing
-
Benjamini, Y., Hochberg, Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. 57, 289-300 (1995).
-
(1995)
J. R. Stat. Soc.
, vol.57
, pp. 289-300
-
-
Benjamini, Y.1
Hochberg, Y.2
-
44
-
-
79952709519
-
PROC: An open-source package for R and S\+ to analyze and compare ROC curves
-
Robin, X. et al. pROC: an open-source package for R and S\+ to analyze and compare ROC curves. BMC Bioinform. 12, 77 (2011).
-
(2011)
BMC Bioinform.
, vol.12
, pp. 77
-
-
Robin, X.1
-
45
-
-
0035942271
-
Significance analysis of microarrays applied to the ionizing radiation response
-
Tusher, V. G., Tibshirani, R., Chu, G. Significance analysis of microarrays applied to the ionizing radiation response. Proc. Natl Acad. Sci. USA 98, 5116-5121 (2001).
-
(2001)
Proc. Natl Acad. Sci. USA
, vol.98
, pp. 5116-5121
-
-
Tusher, V.G.1
Tibshirani, R.2
Chu, G.3
|