-
1
-
-
80755127904
-
The microenvironment in breast cancer progression: biology and implications for treatment
-
Place AE, Jin Huh S, Polyak K. The microenvironment in breast cancer progression: biology and implications for treatment. Breast Cancer Res. 2011;13:227.
-
(2011)
Breast Cancer Res
, vol.13
, pp. 227
-
-
Place, A.E.1
Jin Huh, S.2
Polyak, K.3
-
2
-
-
84875884456
-
Cellular heterogeneity and molecular evolution in cancer
-
Almendro V, Marusyk A, Polyak K. Cellular heterogeneity and molecular evolution in cancer. Annu Rev Pathol. 2013;8:277-302.
-
(2013)
Annu Rev Pathol
, vol.8
, pp. 277-302
-
-
Almendro, V.1
Marusyk, A.2
Polyak, K.3
-
3
-
-
22744445394
-
Determination of stromal signatures in breast carcinoma
-
West RB, Nuyten DSA, Subramanian S, Nielsen TO, Corless CL, Rubin BP, et al. Determination of stromal signatures in breast carcinoma. PLoS Biol. 2005;3, e187.
-
(2005)
PLoS Biol
, vol.3
-
-
West, R.B.1
Nuyten, D.S.A.2
Subramanian, S.3
Nielsen, T.O.4
Corless, C.L.5
Rubin, B.P.6
-
4
-
-
44349174801
-
The fibromatosis signature defines a robust stromal response in breast carcinoma
-
Beck AH, Espinosa I, Gilks CB, van de Rijn M, West RB. The fibromatosis signature defines a robust stromal response in breast carcinoma. Lab Investig. 2008;88:591-601.
-
(2008)
Lab Investig
, vol.88
, pp. 591-601
-
-
Beck, A.H.1
Espinosa, I.2
Gilks, C.B.3
Rijn, M.4
West, R.B.5
-
5
-
-
61349148145
-
The macrophage colony-stimulating factor 1 response signature in breast carcinoma
-
Beck AH, Espinosa I, Edris B, Li R, Montgomery K, Zhu S, et al. The macrophage colony-stimulating factor 1 response signature in breast carcinoma. Clin Cancer Res. 2009;15:778-87.
-
(2009)
Clin Cancer Res
, vol.15
, pp. 778-787
-
-
Beck, A.H.1
Espinosa, I.2
Edris, B.3
Li, R.4
Montgomery, K.5
Zhu, S.6
-
6
-
-
38949202980
-
Extracellular matrix signature identifies breast cancer subgroups with different clinical outcome
-
Bergamaschi A, Tagliabue E, Sørlie T, Naume B, Triulzi T, Orlandi R, et al. Extracellular matrix signature identifies breast cancer subgroups with different clinical outcome. J Pathol. 2008;214:357-67.
-
(2008)
J Pathol
, vol.214
, pp. 357-367
-
-
Bergamaschi, A.1
Tagliabue, E.2
Sørlie, T.3
Naume, B.4
Triulzi, T.5
Orlandi, R.6
-
7
-
-
43249121177
-
Stromal gene expression predicts clinical outcome in breast cancer
-
Finak G, Bertos N, Pepin F, Sadekova S, Souleimanova M, Zhao H, et al. Stromal gene expression predicts clinical outcome in breast cancer. Nat Med. 2008;14:518-27.
-
(2008)
Nat Med
, vol.14
, pp. 518-527
-
-
Finak, G.1
Bertos, N.2
Pepin, F.3
Sadekova, S.4
Souleimanova, M.5
Zhao, H.6
-
8
-
-
81055146760
-
Systematic analysis of breast cancer morphology uncovers stromal features associated with survival
-
Beck AH, Sangoi AR, Leung S, Marinelli RJ, Nielsen TO, van de Vijver MJ, et al. Systematic analysis of breast cancer morphology uncovers stromal features associated with survival. Sci Transl Med. 2011;3:108ra113.
-
(2011)
Sci Transl Med
, vol.3
, pp. 108ra113
-
-
Beck, A.H.1
Sangoi, A.R.2
Leung, S.3
Marinelli, R.J.4
Nielsen, T.O.5
Vijver, M.J.6
-
9
-
-
57149089307
-
Stromal gene signatures in large-B-cell lymphomas
-
Lenz G, Wright G, Dave SS, Xiao W, Powell J, Zhao H, et al. Stromal gene signatures in large-B-cell lymphomas. N Engl J Med. 2008;359:2313-23.
-
(2008)
N Engl J Med
, vol.359
, pp. 2313-2323
-
-
Lenz, G.1
Wright, G.2
Dave, S.S.3
Xiao, W.4
Powell, J.5
Zhao, H.6
-
10
-
-
78049437767
-
Molecular anatomy of breast cancer stroma and its prognostic value in estrogen receptor-positive and -negative cancers
-
Bianchini G, Qi Y, Alvarez RH, Iwamoto T, Coutant C, Ibrahim NK, et al. Molecular anatomy of breast cancer stroma and its prognostic value in estrogen receptor-positive and -negative cancers. J Clin Oncol. 2010;28:4316-23.
-
(2010)
J Clin Oncol
, vol.28
, pp. 4316-4323
-
-
Bianchini, G.1
Qi, Y.2
Alvarez, R.H.3
Iwamoto, T.4
Coutant, C.5
Ibrahim, N.K.6
-
11
-
-
84873503854
-
Significance analysis of prognostic signatures
-
Beck AH, Knoblauch NW, Hefti MM, Kaplan J, Schnitt SJ, Culhane AC, et al. Significance analysis of prognostic signatures. PLoS Comput Biol. 2013;9, e1002875.
-
(2013)
PLoS Comput Biol
, vol.9
-
-
Beck, A.H.1
Knoblauch, N.W.2
Hefti, M.M.3
Kaplan, J.4
Schnitt, S.J.5
Culhane, A.C.6
-
12
-
-
84925818452
-
Stromal gene expression defines poor-prognosis subtypes in colorectal cancer
-
Calon A, Lonardo E, Berenguer-Llergo A, Espinet E, Hernando-Momblona X, Iglesias M, et al. Stromal gene expression defines poor-prognosis subtypes in colorectal cancer. Nat Genet. 2015;47:320-9.
-
(2015)
Nat Genet
, vol.47
, pp. 320-329
-
-
Calon, A.1
Lonardo, E.2
Berenguer-Llergo, A.3
Espinet, E.4
Hernando-Momblona, X.5
Iglesias, M.6
-
14
-
-
78349256721
-
The role of the microenvironment in mammary gland development and cancer
-
Polyak K, Kalluri R. The role of the microenvironment in mammary gland development and cancer. Cold Spring Harb Perspect Biol. 2010;2:a003244.
-
(2010)
Cold Spring Harb Perspect Biol
, vol.2
, pp. a003244
-
-
Polyak, K.1
Kalluri, R.2
-
15
-
-
0037052448
-
Stromal effects on mammary gland development and breast cancer
-
Wiseman BS, Werb Z. Stromal effects on mammary gland development and breast cancer. Science. 2002;296:1046-9.
-
(2002)
Science
, vol.296
, pp. 1046-1049
-
-
Wiseman, B.S.1
Werb, Z.2
-
16
-
-
84858590826
-
Accessories to the crime: functions of cells recruited to the tumor microenvironment
-
Hanahan D, Coussens LM. Accessories to the crime: functions of cells recruited to the tumor microenvironment. Cancer Cell. 2012;21:309-22.
-
(2012)
Cancer Cell
, vol.21
, pp. 309-322
-
-
Hanahan, D.1
Coussens, L.M.2
-
17
-
-
84860697028
-
The tumor microenvironment is a dominant force in multidrug resistance
-
Correia AL, Bissell MJ. The tumor microenvironment is a dominant force in multidrug resistance. Drug Resist Updat. 2012;15:39-49.
-
(2012)
Drug Resist Updat
, vol.15
, pp. 39-49
-
-
Correia, A.L.1
Bissell, M.J.2
-
18
-
-
84864927191
-
An "elite hacker": breast tumors exploit the normal microenvironment program to instruct their progression and biological diversity
-
Boudreau A, van't Veer LJ, Bissell MJ. An "elite hacker": breast tumors exploit the normal microenvironment program to instruct their progression and biological diversity. Cell Adh Migr. 2012;6:236-48.
-
(2012)
Cell Adh Migr
, vol.6
, pp. 236-248
-
-
Boudreau, A.1
Veer, L.J.2
Bissell, M.J.3
-
19
-
-
84864285794
-
Tumour micro-environment elicits innate resistance to RAF inhibitors through HGF secretion
-
Straussman R, Morikawa T, Shee K, Barzily-Rokni M, Qian ZR, Du J, et al. Tumour micro-environment elicits innate resistance to RAF inhibitors through HGF secretion. Nature. 2012;487:500-4.
-
(2012)
Nature
, vol.487
, pp. 500-504
-
-
Straussman, R.1
Morikawa, T.2
Shee, K.3
Barzily-Rokni, M.4
Qian, Z.R.5
Du, J.6
-
21
-
-
63049104211
-
Microenvironmental regulation of metastasis
-
Joyce JA, Pollard JW. Microenvironmental regulation of metastasis. Nat Rev Cancer. 2009;9:239-52.
-
(2009)
Nat Rev Cancer
, vol.9
, pp. 239-252
-
-
Joyce, J.A.1
Pollard, J.W.2
-
22
-
-
34250876926
-
Direct involvement of breast tumor fibroblasts in the modulation of tamoxifen sensitivity
-
Shekhar MPV, Santner S, Carolin KA, Tait L. Direct involvement of breast tumor fibroblasts in the modulation of tamoxifen sensitivity. Am J Pathol. 2007;170:1546-60.
-
(2007)
Am J Pathol
, vol.170
, pp. 1546-1560
-
-
Shekhar, M.P.V.1
Santner, S.2
Carolin, K.A.3
Tait, L.4
-
23
-
-
0025228518
-
Tumor resistance to alkylating agents conferred by mechanisms operative only in vivo
-
Teicher BA, Herman TS, Holden SA, Wang YY, Pfeffer MR, Crawford JW, et al. Tumor resistance to alkylating agents conferred by mechanisms operative only in vivo. Science. 1990;247:1457-61.
-
(1990)
Science
, vol.247
, pp. 1457-1461
-
-
Teicher, B.A.1
Herman, T.S.2
Holden, S.A.3
Wang, Y.Y.4
Pfeffer, M.R.5
Crawford, J.W.6
-
24
-
-
70350721786
-
Crosstalk to stromal fibroblasts induces resistance of lung cancer to epidermal growth factor receptor tyrosine kinase inhibitors
-
Wang W, Li Q, Yamada T, Matsumoto K, Matsumoto I, Oda M, et al. Crosstalk to stromal fibroblasts induces resistance of lung cancer to epidermal growth factor receptor tyrosine kinase inhibitors. Clin Cancer Res. 2009;15:6630-8.
-
(2009)
Clin Cancer Res
, vol.15
, pp. 6630-6638
-
-
Wang, W.1
Li, Q.2
Yamada, T.3
Matsumoto, K.4
Matsumoto, I.5
Oda, M.6
-
25
-
-
9244227134
-
Stromal fibroblasts in cancer initiation and progression
-
Bhowmick NA, Neilson EG, Moses HL. Stromal fibroblasts in cancer initiation and progression. Nature. 2004;432:332-7.
-
(2004)
Nature
, vol.432
, pp. 332-337
-
-
Bhowmick, N.A.1
Neilson, E.G.2
Moses, H.L.3
-
26
-
-
0030575911
-
Laser capture microdissection
-
Emmert-Buck MR, Bonner RF, Smith PD, Chuaqui RF, Zhuang Z, Goldstein SR, et al. Laser capture microdissection. Science. 1996;274:998-1001.
-
(1996)
Science
, vol.274
, pp. 998-1001
-
-
Emmert-Buck, M.R.1
Bonner, R.F.2
Smith, P.D.3
Chuaqui, R.F.4
Zhuang, Z.5
Goldstein, S.R.6
-
27
-
-
79952777929
-
Expression microdissection adapted to commercial laser dissection instruments
-
Hanson JC, Tangrea MA, Kim S, Armani MD, Pohida TJ, Bonner RF, et al. Expression microdissection adapted to commercial laser dissection instruments. Nat Protoc. 2011;6:457-67.
-
(2011)
Nat Protoc
, vol.6
, pp. 457-467
-
-
Hanson, J.C.1
Tangrea, M.A.2
Kim, S.3
Armani, M.D.4
Pohida, T.J.5
Bonner, R.F.6
-
28
-
-
79960936834
-
Immunoguided microdissection techniques
-
Tangrea MA, Hanson JC, Bonner RF, Pohida TJ, Rodriguez-Canales J, Emmert-Buck MR. Immunoguided microdissection techniques. Methods Mol Biol. 2011;755:57-66.
-
(2011)
Methods Mol Biol
, vol.755
, pp. 57-66
-
-
Tangrea, M.A.1
Hanson, J.C.2
Bonner, R.F.3
Pohida, T.J.4
Rodriguez-Canales, J.5
Emmert-Buck, M.R.6
-
29
-
-
84879570392
-
Optimal molecular profiling of tissue and tissue components: defining the best processing and microdissection methods for biomedical applications
-
Rodriguez-Canales J, Hanson JC, Hipp JD, Balis UJ, Tangrea MA, Emmert-Buck MR, et al. Optimal molecular profiling of tissue and tissue components: defining the best processing and microdissection methods for biomedical applications. Methods Mol Biol. 2013;980:61-120.
-
(2013)
Methods Mol Biol
, vol.980
, pp. 61-120
-
-
Rodriguez-Canales, J.1
Hanson, J.C.2
Hipp, J.D.3
Balis, U.J.4
Tangrea, M.A.5
Emmert-Buck, M.R.6
-
30
-
-
80054930037
-
SIVQ-aided laser capture microdissection: a tool for high-throughput expression profiling
-
Hipp J, Cheng J, Hanson JC, Yan W, Taylor P, Hu N, et al. SIVQ-aided laser capture microdissection: a tool for high-throughput expression profiling. J Pathol Inform. 2011;2:19.
-
(2011)
J Pathol Inform
, vol.2
, pp. 19
-
-
Hipp, J.1
Cheng, J.2
Hanson, J.C.3
Yan, W.4
Taylor, P.5
Hu, N.6
-
31
-
-
84897090228
-
Highly multiplexed subcellular RNA sequencing in situ
-
Lee JH, Daugharthy ER, Scheiman J, Kalhor R, Yang JL, Ferrante TC, et al. Highly multiplexed subcellular RNA sequencing in situ. Science. 2014;343:1360-3.
-
(2014)
Science
, vol.343
, pp. 1360-1363
-
-
Lee, J.H.1
Daugharthy, E.R.2
Scheiman, J.3
Kalhor, R.4
Yang, J.L.5
Ferrante, T.C.6
-
32
-
-
84929151009
-
Spatial reconstruction of single-cell gene expression data
-
Satija R, Farrell JA, Gennert D, Schier AF, Regev A. Spatial reconstruction of single-cell gene expression data. Nat Biotechnol. 2015;33:495-502.
-
(2015)
Nat Biotechnol
, vol.33
, pp. 495-502
-
-
Satija, R.1
Farrell, J.A.2
Gennert, D.3
Schier, A.F.4
Regev, A.5
-
33
-
-
84929166604
-
High-throughput spatial mapping of single-cell RNA-seq data to tissue of origin
-
Achim K, Pettit J-B, Saraiva LR, Gavriouchkina D, Larsson T, Arendt D, et al. High-throughput spatial mapping of single-cell RNA-seq data to tissue of origin. Nat Biotechnol. 2015;33:503-9.
-
(2015)
Nat Biotechnol
, vol.33
, pp. 503-509
-
-
Achim, K.1
Pettit, J.-B.2
Saraiva, L.R.3
Gavriouchkina, D.4
Larsson, T.5
Arendt, D.6
-
35
-
-
84897402237
-
Next-gen immunohistochemistry
-
Rimm DL. Next-gen immunohistochemistry. Nat Methods. 2014;11:381-3.
-
(2014)
Nat Methods
, vol.11
, pp. 381-383
-
-
Rimm, D.L.1
-
36
-
-
84898402897
-
Multiplexed ion beam imaging of human breast tumors
-
Angelo M, Bendall SC, Finck R, Hale MB, Hitzman C, Borowsky AD, et al. Multiplexed ion beam imaging of human breast tumors. Nat Med. 2014;20:436-42.
-
(2014)
Nat Med
, vol.20
, pp. 436-442
-
-
Angelo, M.1
Bendall, S.C.2
Finck, R.3
Hale, M.B.4
Hitzman, C.5
Borowsky, A.D.6
-
37
-
-
84897954497
-
Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry
-
Giesen C, Wang HAO, Schapiro D, Zivanovic N, Jacobs A, Hattendorf B, et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nat Methods. 2014;11:417-22.
-
(2014)
Nat Methods
, vol.11
, pp. 417-422
-
-
Giesen, C.1
Wang, H.A.O.2
Schapiro, D.3
Zivanovic, N.4
Jacobs, A.5
Hattendorf, B.6
-
38
-
-
3142512612
-
Molecular characterization of the tumor microenvironment in breast cancer
-
Allinen M, Beroukhim R, Cai L, Brennan C, Lahti-Domenici J, Huang H, et al. Molecular characterization of the tumor microenvironment in breast cancer. Cancer Cell. 2004;6:17-32.
-
(2004)
Cancer Cell
, vol.6
, pp. 17-32
-
-
Allinen, M.1
Beroukhim, R.2
Cai, L.3
Brennan, C.4
Lahti-Domenici, J.5
Huang, H.6
-
39
-
-
39649088238
-
A stromal gene signature associated with inflammatory breast cancer
-
Boersma BJ, Reimers M, Yi M, Ludwig JA, Luke BT, Stephens RM, et al. A stromal gene signature associated with inflammatory breast cancer. Int J Cancer. 2008;122:1324-32.
-
(2008)
Int J Cancer
, vol.122
, pp. 1324-1332
-
-
Boersma, B.J.1
Reimers, M.2
Yi, M.3
Ludwig, J.A.4
Luke, B.T.5
Stephens, R.M.6
-
40
-
-
33751312857
-
Gene expression signatures of morphologically normal breast tissue identify basal-like tumors
-
Finak G, Sadekova S, Pepin F, Hallett M, Meterissian S, Halwani F, et al. Gene expression signatures of morphologically normal breast tissue identify basal-like tumors. Breast Cancer Res. 2006;8:R58.
-
(2006)
Breast Cancer Res
, vol.8
, pp. R58
-
-
Finak, G.1
Sadekova, S.2
Pepin, F.3
Hallett, M.4
Meterissian, S.5
Halwani, F.6
-
41
-
-
84865137131
-
Gene expression profiling of tumour epithelial and stromal compartments during breast cancer progression
-
Vargas AC, McCart Reed AE, Waddell N, Lane A, Reid LE, Smart CE, et al. Gene expression profiling of tumour epithelial and stromal compartments during breast cancer progression. Breast Cancer Res Treat. 2012;135:153-65.
-
(2012)
Breast Cancer Res Treat
, vol.135
, pp. 153-165
-
-
Vargas, A.C.1
McCart Reed, A.E.2
Waddell, N.3
Lane, A.4
Reid, L.E.5
Smart, C.E.6
-
42
-
-
84865773617
-
Differentially expressed genes regulating the progression of ductal carcinoma in situ to invasive breast cancer
-
Lee S, Stewart S, Nagtegaal I, Luo J, Wu Y, Colditz G, et al. Differentially expressed genes regulating the progression of ductal carcinoma in situ to invasive breast cancer. Cancer Res. 2012;72:4574-86.
-
(2012)
Cancer Res
, vol.72
, pp. 4574-4586
-
-
Lee, S.1
Stewart, S.2
Nagtegaal, I.3
Luo, J.4
Wu, Y.5
Colditz, G.6
-
43
-
-
58849114639
-
Molecular signatures suggest a major role for stromal cells in development of invasive breast cancer
-
Casey T, Bond J, Tighe S, Hunter T, Lintault L, Patel O, et al. Molecular signatures suggest a major role for stromal cells in development of invasive breast cancer. Breast Cancer Res Treat. 2009;114:47-62.
-
(2009)
Breast Cancer Res Treat
, vol.114
, pp. 47-62
-
-
Casey, T.1
Bond, J.2
Tighe, S.3
Hunter, T.4
Lintault, L.5
Patel, O.6
-
44
-
-
79952635505
-
Principles and strategies for developing network models in cancer
-
Pe'er D, Hacohen N. Principles and strategies for developing network models in cancer. Cell. 2011;144:864-73.
-
(2011)
Cell
, vol.144
, pp. 864-873
-
-
Pe'er, D.1
Hacohen, N.2
-
46
-
-
84855378129
-
NEW: network-enabled wisdom in biology, medicine, and health care
-
Schadt EE, Björkegren JLM. NEW: network-enabled wisdom in biology, medicine, and health care. Sci Transl Med. 2012;4:115rv1.
-
(2012)
Sci Transl Med
, vol.4
-
-
Schadt, E.E.1
Björkegren, J.L.M.2
-
47
-
-
84876907931
-
Integrated systems approach identifies genetic nodes and networks in late-onset Alzheimer's disease
-
Zhang B, Gaiteri C, Bodea L-G, Wang Z, McElwee J, Podtelezhnikov AA, et al. Integrated systems approach identifies genetic nodes and networks in late-onset Alzheimer's disease. Cell. 2013;153:707-20.
-
(2013)
Cell
, vol.153
, pp. 707-720
-
-
Zhang, B.1
Gaiteri, C.2
Bodea, L.-G.3
Wang, Z.4
McElwee, J.5
Podtelezhnikov, A.A.6
-
49
-
-
84885131104
-
Correlating transcriptional networks to breast cancer survival: a large-scale coexpression analysis
-
Clarke C, Madden SF, Doolan P, Aherne ST, Joyce H, O'Driscoll L, et al. Correlating transcriptional networks to breast cancer survival: a large-scale coexpression analysis. Carcinogenesis. 2013;34:2300-8.
-
(2013)
Carcinogenesis
, vol.34
, pp. 2300-2308
-
-
Clarke, C.1
Madden, S.F.2
Doolan, P.3
Aherne, S.T.4
Joyce, H.5
O'Driscoll, L.6
-
50
-
-
84880014085
-
Coexpression analysis of large cancer datasets provides insight into the cellular phenotypes of the tumour microenvironment
-
Doig TN, Hume DA, Theocharidis T, Goodlad JR, Gregory CD, Freeman TC. Coexpression analysis of large cancer datasets provides insight into the cellular phenotypes of the tumour microenvironment. BMC Genomics. 2013;14:469.
-
(2013)
BMC Genomics
, vol.14
, pp. 469
-
-
Doig, T.N.1
Hume, D.A.2
Theocharidis, T.3
Goodlad, J.R.4
Gregory, C.D.5
Freeman, T.C.6
-
51
-
-
57149110826
-
The Human Protein Atlas-a tool for pathology
-
Pontén F, Jirström K, Uhlen M. The Human Protein Atlas-a tool for pathology. J Pathol. 2008;216:387-93.
-
(2008)
J Pathol
, vol.216
, pp. 387-393
-
-
Pontén, F.1
Jirström, K.2
Uhlen, M.3
-
52
-
-
84920269464
-
Tissue-based map of the human proteome
-
Uhlen M, Fagerberg L, Hallstrom BM, Lindskog C, Oksvold P, Mardinoglu A, et al. Tissue-based map of the human proteome. Science. 2015;347:1260419.
-
(2015)
Science
, vol.347
, pp. 1260419
-
-
Uhlen, M.1
Fagerberg, L.2
Hallstrom, B.M.3
Lindskog, C.4
Oksvold, P.5
Mardinoglu, A.6
-
53
-
-
0036081355
-
Gene Expression Omnibus: NCBI gene expression and hybridization array data repository
-
Edgar R, Domrachev M, Lash AE. Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res. 2002;30:207-10.
-
(2002)
Nucleic Acids Res
, vol.30
, pp. 207-210
-
-
Edgar, R.1
Domrachev, M.2
Lash, A.E.3
-
54
-
-
67549125238
-
Gene expression profiling of the tumor microenvironment during breast cancer progression
-
Ma X-J, Dahiya S, Richardson E, Erlander M, Sgroi DC. Gene expression profiling of the tumor microenvironment during breast cancer progression. Breast Cancer Res. 2009;11:R7.
-
(2009)
Breast Cancer Res
, vol.11
, pp. R7
-
-
Ma, X.-J.1
Dahiya, S.2
Richardson, E.3
Erlander, M.4
Sgroi, D.C.5
-
55
-
-
35748982114
-
AILUN: reannotating gene expression data automatically
-
Chen R, Li L, Butte AJ. AILUN: reannotating gene expression data automatically. Nat Methods. 2007;4:879.
-
(2007)
Nat Methods
, vol.4
, pp. 879
-
-
Chen, R.1
Li, L.2
Butte, A.J.3
-
56
-
-
77956873627
-
Tackling the widespread and critical impact of batch effects in high-throughput data
-
Leek JT, Scharpf RB, Bravo HC, Simcha D, Langmead B, Johnson WE, et al. Tackling the widespread and critical impact of batch effects in high-throughput data. Nat Rev Genet. 2010;11:733-9.
-
(2010)
Nat Rev Genet
, vol.11
, pp. 733-739
-
-
Leek, J.T.1
Scharpf, R.B.2
Bravo, H.C.3
Simcha, D.4
Langmead, B.5
Johnson, W.E.6
-
57
-
-
84861153094
-
Matrix eQTL: ultra fast eQTL analysis via large matrix operations
-
Shabalin AA. Matrix eQTL: ultra fast eQTL analysis via large matrix operations. Bioinformatics. 2012;28:1353-8.
-
(2012)
Bioinformatics
, vol.28
, pp. 1353-1358
-
-
Shabalin, A.A.1
-
59
-
-
84859935998
-
RedeR: R/Bioconductor package for representing modular structures, nested networks and multiple levels of hierarchical associations
-
Castro MAA, Wang X, Fletcher MNC, Meyer KB, Markowetz F. RedeR: R/Bioconductor package for representing modular structures, nested networks and multiple levels of hierarchical associations. Genome Biol. 2012;13:R29.
-
(2012)
Genome Biol
, vol.13
, pp. R29
-
-
Castro, M.A.A.1
Wang, X.2
Fletcher, M.N.C.3
Meyer, K.B.4
Markowetz, F.5
-
60
-
-
84907572339
-
SANTA: quantifying the functional content of molecular networks
-
Cornish AJ, Markowetz F. SANTA: quantifying the functional content of molecular networks. PLoS Comput Biol. 2014;10, e1003808.
-
(2014)
PLoS Comput Biol
, vol.10
-
-
Cornish, A.J.1
Markowetz, F.2
-
61
-
-
84914179053
-
-
Vienna, Austria: R Foundation for Statistical Computing
-
R Foundation for Statistical Computing. R: A Language and Environment for Statistical Computing. Vienna, Austria: R Foundation for Statistical Computing; 2014.
-
(2014)
R: A Language and Environment for Statistical Computing
-
-
-
62
-
-
11144358198
-
A gene atlas of the mouse and human protein-encoding transcriptomes
-
Su AI, Wiltshire T, Batalov S, Lapp H, Ching KA, Block D, et al. A gene atlas of the mouse and human protein-encoding transcriptomes. Proc Natl Acad Sci U S A. 2004;101:6062-7.
-
(2004)
Proc Natl Acad Sci U S A
, vol.101
, pp. 6062-6067
-
-
Su, A.I.1
Wiltshire, T.2
Batalov, S.3
Lapp, H.4
Ching, K.A.5
Block, D.6
-
63
-
-
0004594704
-
Nerve growth factor stimulates proliferation and survival of human breast cancer cells through two distinct signaling pathways
-
Descamps S, Toillon RA, Adriaenssens E, Pawlowski V, Cool SM, Nurcombe V, et al. Nerve growth factor stimulates proliferation and survival of human breast cancer cells through two distinct signaling pathways. J Biol Chem. 2001;276:17864-70.
-
(2001)
J Biol Chem
, vol.276
, pp. 17864-17870
-
-
Descamps, S.1
Toillon, R.A.2
Adriaenssens, E.3
Pawlowski, V.4
Cool, S.M.5
Nurcombe, V.6
-
64
-
-
84866484322
-
Biological influence of brain-derived neurotrophic factor on breast cancer cells
-
Yang X, Martin TA, Jiang WG. Biological influence of brain-derived neurotrophic factor on breast cancer cells. Int J Oncol. 2012;41:1541-6.
-
(2012)
Int J Oncol
, vol.41
, pp. 1541-1546
-
-
Yang, X.1
Martin, T.A.2
Jiang, W.G.3
-
65
-
-
79953300722
-
Brain-derived neurotrophic factor and neurotrophin-4/5 are expressed in breast cancer and can be targeted to inhibit tumor cell survival
-
Vanhecke E, Adriaenssens E, Verbeke S, Meignan S, Germain E, Berteaux N, et al. Brain-derived neurotrophic factor and neurotrophin-4/5 are expressed in breast cancer and can be targeted to inhibit tumor cell survival. Clin Cancer Res. 2011;17:1741-52.
-
(2011)
Clin Cancer Res
, vol.17
, pp. 1741-1752
-
-
Vanhecke, E.1
Adriaenssens, E.2
Verbeke, S.3
Meignan, S.4
Germain, E.5
Berteaux, N.6
-
66
-
-
84881528430
-
MicroRNA-191, an estrogen-responsive microRNA, functions as an oncogenic regulator in human breast cancer
-
Nagpal N, Ahmad HM, Molparia B, Kulshreshtha R. MicroRNA-191, an estrogen-responsive microRNA, functions as an oncogenic regulator in human breast cancer. Carcinogenesis. 2013;34:1889-99.
-
(2013)
Carcinogenesis
, vol.34
, pp. 1889-1899
-
-
Nagpal, N.1
Ahmad, H.M.2
Molparia, B.3
Kulshreshtha, R.4
-
67
-
-
23844555119
-
MicroRNA gene expression deregulation in human breast cancer
-
Iorio MV, Ferracin M, Liu C-G, Veronese A, Spizzo R, Sabbioni S, et al. MicroRNA gene expression deregulation in human breast cancer. Cancer Res. 2005;65:7065-70.
-
(2005)
Cancer Res
, vol.65
, pp. 7065-7070
-
-
Iorio, M.V.1
Ferracin, M.2
Liu, C.-G.3
Veronese, A.4
Spizzo, R.5
Sabbioni, S.6
-
68
-
-
79960557212
-
Brain-derived neurotrophic factor expression predicts adverse pathological & clinical outcomes in human breast cancer
-
Patani N, Jiang WG, Mokbel K. Brain-derived neurotrophic factor expression predicts adverse pathological & clinical outcomes in human breast cancer. Cancer Cell Int. 2011;11:23.
-
(2011)
Cancer Cell Int
, vol.11
, pp. 23
-
-
Patani, N.1
Jiang, W.G.2
Mokbel, K.3
-
69
-
-
84859107394
-
Metabotropic glutamate receptor-1: a potential therapeutic target for the treatment of breast cancer
-
Speyer CL, Smith JS, Banda M, DeVries JA, Mekani T, Gorski DH. Metabotropic glutamate receptor-1: a potential therapeutic target for the treatment of breast cancer. Breast Cancer Res Treat. 2012;132:565-73.
-
(2012)
Breast Cancer Res Treat
, vol.132
, pp. 565-573
-
-
Speyer, C.L.1
Smith, J.S.2
Banda, M.3
DeVries, J.A.4
Mekani, T.5
Gorski, D.H.6
-
70
-
-
0141816752
-
EZH2 is a marker of aggressive breast cancer and promotes neoplastic transformation of breast epithelial cells
-
Kleer CG, Cao Q, Varambally S, Shen R, Ota I, Tomlins SA, et al. EZH2 is a marker of aggressive breast cancer and promotes neoplastic transformation of breast epithelial cells. Proc Natl Acad Sci U S A. 2003;100:11606-11.
-
(2003)
Proc Natl Acad Sci U S A
, vol.100
, pp. 11606-11611
-
-
Kleer, C.G.1
Cao, Q.2
Varambally, S.3
Shen, R.4
Ota, I.5
Tomlins, S.A.6
-
71
-
-
60149096212
-
Downregulation of EZH2 decreases growth of estrogen receptor-negative invasive breast carcinoma and requires BRCA1
-
Gonzalez ME, Li X, Toy K, DuPrie M, Ventura AC, Banerjee M, et al. Downregulation of EZH2 decreases growth of estrogen receptor-negative invasive breast carcinoma and requires BRCA1. Oncogene. 2009;28:843-53.
-
(2009)
Oncogene
, vol.28
, pp. 843-853
-
-
Gonzalez, M.E.1
Li, X.2
Toy, K.3
DuPrie, M.4
Ventura, A.C.5
Banerjee, M.6
-
73
-
-
0033982936
-
KEGG: Kyoto Encyclopedia Of Genes And Genomes
-
Kanehisa M, Goto S. KEGG: Kyoto Encyclopedia Of Genes And Genomes. Nucleic Acids Res. 2000;28:27-30.
-
(2000)
Nucleic Acids Res
, vol.28
, pp. 27-30
-
-
Kanehisa, M.1
Goto, S.2
-
74
-
-
84907964639
-
The prognostic ease and difficulty of invasive breast carcinoma
-
Tofigh A, Suderman M, Paquet ER, Livingstone J, Bertos N, Saleh SM, et al. The prognostic ease and difficulty of invasive breast carcinoma. Cell Rep. 2014;9:129-42.
-
(2014)
Cell Rep
, vol.9
, pp. 129-142
-
-
Tofigh, A.1
Suderman, M.2
Paquet, E.R.3
Livingstone, J.4
Bertos, N.5
Saleh, S.M.6
-
75
-
-
41449118521
-
Module map of stem cell genes guides creation of epithelial cancer stem cells
-
Wong DJ, Liu H, Ridky TW, Cassarino D, Segal E, Chang HY. Module map of stem cell genes guides creation of epithelial cancer stem cells. Cell Stem Cell. 2008;2:333-44.
-
(2008)
Cell Stem Cell
, vol.2
, pp. 333-344
-
-
Wong, D.J.1
Liu, H.2
Ridky, T.W.3
Cassarino, D.4
Segal, E.5
Chang, H.Y.6
-
76
-
-
33144462268
-
Gene expression profiling in breast cancer: understanding the molecular basis of histologic grade to improve prognosis
-
Sotiriou C, Wirapati P, Loi S, Harris A, Fox S, Smeds J, et al. Gene expression profiling in breast cancer: understanding the molecular basis of histologic grade to improve prognosis. J Natl Cancer Inst. 2006;98:262-72.
-
(2006)
J Natl Cancer Inst
, vol.98
, pp. 262-272
-
-
Sotiriou, C.1
Wirapati, P.2
Loi, S.3
Harris, A.4
Fox, S.5
Smeds, J.6
-
77
-
-
33748286796
-
A signature of chromosomal instability inferred from gene expression profiles predicts clinical outcome in multiple human cancers
-
Carter SL, Eklund AC, Kohane IS, Harris LN, Szallasi Z. A signature of chromosomal instability inferred from gene expression profiles predicts clinical outcome in multiple human cancers. Nat Genet. 2006;38:1043-8.
-
(2006)
Nat Genet
, vol.38
, pp. 1043-1048
-
-
Carter, S.L.1
Eklund, A.C.2
Kohane, I.S.3
Harris, L.N.4
Szallasi, Z.5
-
78
-
-
84870917775
-
Epithelial-stromal interactions in human breast cancer: effects on adhesion, plasma membrane fluidity and migration speed and directness
-
Angelucci C, Maulucci G, Lama G, Proietti G, Colabianchi A, Papi M, et al. Epithelial-stromal interactions in human breast cancer: effects on adhesion, plasma membrane fluidity and migration speed and directness. PLoS One. 2012;7, e50804.
-
(2012)
PLoS One
, vol.7
-
-
Angelucci, C.1
Maulucci, G.2
Lama, G.3
Proietti, G.4
Colabianchi, A.5
Papi, M.6
-
79
-
-
70149111933
-
Systems-level modeling of cancer-fibroblast interaction
-
Wadlow RC, Wittner BS, Finley SA, Bergquist H, Upadhyay R, Finn S, et al. Systems-level modeling of cancer-fibroblast interaction. PLoS One. 2009;4, e6888.
-
(2009)
PLoS One
, vol.4
-
-
Wadlow, R.C.1
Wittner, B.S.2
Finley, S.A.3
Bergquist, H.4
Upadhyay, R.5
Finn, S.6
-
80
-
-
0029058653
-
Co-culture of human breast adenocarcinoma MCF-7 cells and human dermal fibroblasts enhances the production of matrix metalloproteinases 1, 2 and 3 in fibroblasts
-
Ito A, Nakajima S, Sasaguri Y, Nagase H, Mori Y. Co-culture of human breast adenocarcinoma MCF-7 cells and human dermal fibroblasts enhances the production of matrix metalloproteinases 1, 2 and 3 in fibroblasts. Br J Cancer. 1995;71:1039-45.
-
(1995)
Br J Cancer
, vol.71
, pp. 1039-1045
-
-
Ito, A.1
Nakajima, S.2
Sasaguri, Y.3
Nagase, H.4
Mori, Y.5
-
81
-
-
78751521504
-
Interactions with fibroblasts are distinct in basal-like and luminal breast cancers
-
Camp JT, Elloumi F, Roman-Perez E, Rein J, Stewart DA, Harrell JC, et al. Interactions with fibroblasts are distinct in basal-like and luminal breast cancers. Mol Cancer Res. 2011;9:3-13.
-
(2011)
Mol Cancer Res
, vol.9
, pp. 3-13
-
-
Camp, J.T.1
Elloumi, F.2
Roman-Perez, E.3
Rein, J.4
Stewart, D.A.5
Harrell, J.C.6
-
82
-
-
0141993704
-
A gene-coexpression network for global discovery of conserved genetic modules
-
Stuart JM, Segal E, Koller D, Kim SK. A gene-coexpression network for global discovery of conserved genetic modules. Science. 2003;302:249-55.
-
(2003)
Science
, vol.302
, pp. 249-255
-
-
Stuart, J.M.1
Segal, E.2
Koller, D.3
Kim, S.K.4
-
83
-
-
0037941585
-
Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data
-
Segal E, Shapira M, Regev A, Pe'er D, Botstein D, Koller D, et al. Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data. Nat Genet. 2003;34:166-76.
-
(2003)
Nat Genet
, vol.34
, pp. 166-176
-
-
Segal, E.1
Shapira, M.2
Regev, A.3
Pe'er, D.4
Botstein, D.5
Koller, D.6
-
84
-
-
23944458138
-
A general framework for weighted gene co-expression network analysis
-
Zhang B, Horvath S. A general framework for weighted gene co-expression network analysis. Stat Appl Genet Mol Biol. 2005;4:Article17.
-
(2005)
Stat Appl Genet Mol Biol
, vol.4
-
-
Zhang, B.1
Horvath, S.2
-
85
-
-
34247864012
-
Three-dimensional culture models of normal and malignant breast epithelial cells
-
Lee GY, Kenny PA, Lee EH, Bissell MJ. Three-dimensional culture models of normal and malignant breast epithelial cells. Nat Methods. 2007;4:359-65.
-
(2007)
Nat Methods
, vol.4
, pp. 359-365
-
-
Lee, G.Y.1
Kenny, P.A.2
Lee, E.H.3
Bissell, M.J.4
-
86
-
-
84911966357
-
Cancer exosomes perform cell-independent microRNA biogenesis and promote tumorigenesis
-
Melo SA, Sugimoto H, O'Connell JT, Kato N, Villanueva A, Vidal A, et al. Cancer exosomes perform cell-independent microRNA biogenesis and promote tumorigenesis. Cancer Cell. 2014;26:707-21.
-
(2014)
Cancer Cell
, vol.26
, pp. 707-721
-
-
Melo, S.A.1
Sugimoto, H.2
O'Connell, J.T.3
Kato, N.4
Villanueva, A.5
Vidal, A.6
-
87
-
-
84908275360
-
Exosome transfer from stromal to breast cancer cells regulates therapy resistance pathways
-
Boelens MC, Wu TJ, Nabet BY, Xu B, Qiu Y, Yoon T, et al. Exosome transfer from stromal to breast cancer cells regulates therapy resistance pathways. Cell. 2014;159:499-513.
-
(2014)
Cell
, vol.159
, pp. 499-513
-
-
Boelens, M.C.1
Wu, T.J.2
Nabet, B.Y.3
Xu, B.4
Qiu, Y.5
Yoon, T.6
-
88
-
-
0037456823
-
Genetics of gene expression surveyed in maize, mouse and man
-
Schadt EE, Monks SA, Drake TA, Lusis AJ, Che N, Colinayo V, et al. Genetics of gene expression surveyed in maize, mouse and man. Nature. 2003;422:297-302.
-
(2003)
Nature
, vol.422
, pp. 297-302
-
-
Schadt, E.E.1
Monks, S.A.2
Drake, T.A.3
Lusis, A.J.4
Che, N.5
Colinayo, V.6
-
89
-
-
41349095280
-
Genetics of gene expression and its effect on disease
-
Emilsson V, Thorleifsson G, Zhang B, Leonardson AS, Zink F, Zhu J, et al. Genetics of gene expression and its effect on disease. Nature. 2008;452:423-8.
-
(2008)
Nature
, vol.452
, pp. 423-428
-
-
Emilsson, V.1
Thorleifsson, G.2
Zhang, B.3
Leonardson, A.S.4
Zink, F.5
Zhu, J.6
-
90
-
-
79952536908
-
Microenvironmental influences that drive progression from benign breast disease to invasive breast cancer
-
Cichon MA, Degnim AC, Visscher DW, Radisky DC. Microenvironmental influences that drive progression from benign breast disease to invasive breast cancer. J Mammary Gland Biol Neoplasia. 2010;15:389-97.
-
(2010)
J Mammary Gland Biol Neoplasia
, vol.15
, pp. 389-397
-
-
Cichon, M.A.1
Degnim, A.C.2
Visscher, D.W.3
Radisky, D.C.4
-
91
-
-
17444400095
-
BIAS: Bioinformatics Integrated Application Software
-
Finak G, Godin N, Hallett M, Pepin F, Rajabi Z, Srivastava V, et al. BIAS: Bioinformatics Integrated Application Software. Bioinformatics. 2005;21:1745-6.
-
(2005)
Bioinformatics
, vol.21
, pp. 1745-1746
-
-
Finak, G.1
Godin, N.2
Hallett, M.3
Pepin, F.4
Rajabi, Z.5
Srivastava, V.6
-
92
-
-
12344280017
-
Summaries of Affymetrix GeneChip probe level data
-
Irizarry RA, Bolstad BM, Collin F, Cope LM, Hobbs B, Speed TP. Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res. 2003;31, e15.
-
(2003)
Nucleic Acids Res
, vol.31
-
-
Irizarry, R.A.1
Bolstad, B.M.2
Collin, F.3
Cope, L.M.4
Hobbs, B.5
Speed, T.P.6
-
93
-
-
0142121516
-
Exploration, normalization, and summaries of high density oligonucleotide array probe level data
-
Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, Scherf U, et al. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics. 2003;4:249-64.
-
(2003)
Biostatistics
, vol.4
, pp. 249-264
-
-
Irizarry, R.A.1
Hobbs, B.2
Collin, F.3
Beazer-Barclay, Y.D.4
Antonellis, K.J.5
Scherf, U.6
-
94
-
-
0242333835
-
Normalization of cDNA microarray data
-
Smyth GK, Speed T. Normalization of cDNA microarray data. Methods. 2003;31:265-73.
-
(2003)
Methods
, vol.31
, pp. 265-273
-
-
Smyth, G.K.1
Speed, T.2
|