Journal Article
. 2008 Jul;10(4).
doi: 10.1186/bcr2124.

Meta-analysis of gene expression profiles in breast cancer: toward a unified understanding of breast cancer subtyping and prognosis signatures

Pratyaksha Wirapati 1 Christos Sotiriou  Susanne Kunkel  Pierre Farmer  Sylvain Pradervand  Benjamin Haibe-Kains  Christine Desmedt  Michail Ignatiadis  Thierry Sengstag  Frédéric Schütz  Darlene R Goldstein  Martine Piccart  Mauro Delorenzi  
Affiliations
  • PMID: 18662380
  •     39 References
  •     337 citations

Abstract

Introduction: Breast cancer subtyping and prognosis have been studied extensively by gene expression profiling, resulting in disparate signatures with little overlap in their constituent genes. Although a previous study demonstrated a prognostic concordance among gene expression signatures, it was limited to only one dataset and did not fully elucidate how the different genes were related to one another nor did it examine the contribution of well-known biological processes of breast cancer tumorigenesis to their prognostic performance.

Method: To address the above issues and to further validate these initial findings, we performed the largest meta-analysis of publicly available breast cancer gene expression and clinical data, which are comprised of 2,833 breast tumors. Gene coexpression modules of three key biological processes in breast cancer (namely, proliferation, estrogen receptor [ER], and HER2 signaling) were used to dissect the role of constituent genes of nine prognostic signatures.

Results: Using a meta-analytical approach, we consolidated the signatures associated with ER signaling, ERBB2 amplification, and proliferation. Previously published expression-based nomenclature of breast cancer 'intrinsic' subtypes can be mapped to the three modules, namely, the ER-/HER2- (basal-like), the HER2+ (HER2-like), and the low- and high-proliferation ER+/HER2- subtypes (luminal A and B). We showed that all nine prognostic signatures exhibited a similar prognostic performance in the entire dataset. Their prognostic abilities are due mostly to the detection of proliferation activity. Although ER- status (basal-like) and ERBB2+ expression status correspond to bad outcome, they seem to act through elevated expression of proliferation genes and thus contain only indirect information about prognosis. Clinical variables measuring the extent of tumor progression, such as tumor size and nodal status, still add independent prognostic information to proliferation genes.

Conclusion: This meta-analysis unifies various results of previous gene expression studies in breast cancer. It reveals connections between traditional prognostic factors, expression-based subtyping, and prognostic signatures, highlighting the important role of proliferation in breast cancer prognosis.

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Highly Cited.
A pharmacogenomic method for individualized prediction of drug sensitivity.
Adam L Cohen, Raffaella Soldi, +8 authors, Andrea H Bild.
Mol Syst Biol, 2011 Jul 21; 7. PMID: 21772261    Free PMC article.
A simple method for assigning genomic grade to individual breast tumours.
Kristian Wennmalm, Jonas Bergh.
BMC Cancer, 2011 Jul 23; 11. PMID: 21777443    Free PMC article.
Microarrays in the 2010s: the contribution of microarray-based gene expression profiling to breast cancer classification, prognostication and prediction.
Pierre-Emmanuel Colombo, Fernanda Milanezi, Britta Weigelt, Jorge S Reis-Filho.
Breast Cancer Res, 2011 Jul 27; 13(3). PMID: 21787441    Free PMC article.
Review.
Consistent metagenes from cancer expression profiles yield agent specific predictors of chemotherapy response.
Qiyuan Li, Aron C Eklund, +8 authors, Zoltan Szallasi.
BMC Bioinformatics, 2011 Jul 30; 12. PMID: 21798043    Free PMC article.
Microarray-based oncogenic pathway profiling in advanced serous papillary ovarian carcinoma.
Xuan Bich Trinh, Wiebren A A Tjalma, +8 authors, Peter A van Dam.
PLoS One, 2011 Jul 30; 6(7). PMID: 21799864    Free PMC article.
Induction of stable drug resistance in human breast cancer cells using a combinatorial zinc finger transcription factor library.
Jeongeun Lee, Andrew S Hirsh, +9 authors, Dennis C Sgroi.
PLoS One, 2011 Aug 06; 6(7). PMID: 21818254    Free PMC article.
Challenges translating breast cancer gene signatures into the clinic.
Britta Weigelt, Lajos Pusztai, Alan Ashworth, Jorge S Reis-Filho.
Nat Rev Clin Oncol, 2011 Sep 01; 9(1). PMID: 21878891
Review.
DNA methylation profiling reveals a predominant immune component in breast cancers.
Sarah Dedeurwaerder, Christine Desmedt, +23 authors, François Fuks.
EMBO Mol Med, 2011 Sep 13; 3(12). PMID: 21910250    Free PMC article.
Highly Cited.
Breast cancer - one term, many entities?
Nicholas R Bertos, Morag Park.
J Clin Invest, 2011 Oct 04; 121(10). PMID: 21965335    Free PMC article.
Highly Cited. Review.
Insight into the heterogeneity of breast cancer through next-generation sequencing.
Hege G Russnes, Nicholas Navin, James Hicks, Anne-Lise Borresen-Dale.
J Clin Invest, 2011 Oct 04; 121(10). PMID: 21965338    Free PMC article.
Highly Cited. Review.
A clinically relevant gene signature in triple negative and basal-like breast cancer.
Achim Rody, Thomas Karn, +11 authors, Manfred Kaufmann.
Breast Cancer Res, 2011 Oct 08; 13(5). PMID: 21978456    Free PMC article.
Highly Cited.
Prognostic and predictive role of ESR1 status for postmenopausal patients with endocrine-responsive early breast cancer in the Danish cohort of the BIG 1-98 trial.
B Ejlertsen, J Aldridge, +10 authors, Danish Breast Cancer Cooperative Group the BIG 1-98 Collaborative Group and the International Breast Cancer Study Group.
Ann Oncol, 2011 Oct 12; 23(5). PMID: 21986093    Free PMC article.
RUNX1 and its understudied role in breast cancer.
Kevin A Janes.
Cell Cycle, 2011 Oct 26; 10(20). PMID: 22024923    Free PMC article.
Most random gene expression signatures are significantly associated with breast cancer outcome.
David Venet, Jacques E Dumont, Vincent Detours.
PLoS Comput Biol, 2011 Oct 27; 7(10). PMID: 22028643    Free PMC article.
Highly Cited.
Ki-67: level of evidence and methodological considerations for its role in the clinical management of breast cancer: analytical and critical review.
Elisabeth Luporsi, Fabrice André, +22 authors, Jean-Pierre Bellocq.
Breast Cancer Res Treat, 2011 Nov 04; 132(3). PMID: 22048814    Free PMC article.
Highly Cited. Review.
Targeted therapies: how personal should we go?
Miriam Martini, Loredana Vecchione, +2 authors, Alberto Bardelli.
Nat Rev Clin Oncol, 2011 Nov 16; 9(2). PMID: 22083042
Review.
Meta-analysis of phase III trials of docetaxel alone or in combination with chemotherapy in metastatic breast cancer.
Maurizio Belfiglio, Caterina Fanizza, +4 authors, Consorzio Interuniversitario Nazionale per la Bio-Oncologia (CINBO).
J Cancer Res Clin Oncol, 2011 Nov 19; 138(2). PMID: 22095437    Free PMC article.
Systematic Review.
MetaQC: objective quality control and inclusion/exclusion criteria for genomic meta-analysis.
Dongwan D Kang, Etienne Sibille, Naftali Kaminski, George C Tseng.
Nucleic Acids Res, 2011 Nov 26; 40(2). PMID: 22116060    Free PMC article.
Multiple-input multiple-output causal strategies for gene selection.
Gianluca Bontempi, Benjamin Haibe-Kains, +2 authors, John Quackenbush.
BMC Bioinformatics, 2011 Nov 29; 12. PMID: 22118187    Free PMC article.
Invasive Breast Cancer: Recognition of Molecular Subtypes.
Johanna D Strehl, David L Wachter, +2 authors, Arndt Hartmann.
Breast Care (Basel), 2011 Dec 03; 6(4). PMID: 22135623    Free PMC article.
Practical implications of gene-expression-based assays for breast oncologists.
Aleix Prat, Matthew J Ellis, Charles M Perou.
Nat Rev Clin Oncol, 2011 Dec 07; 9(1). PMID: 22143140    Free PMC article.
Highly Cited. Review.
Empirical comparison of cross-platform normalization methods for gene expression data.
Jason Rudy, Faramarz Valafar.
BMC Bioinformatics, 2011 Dec 14; 12. PMID: 22151536    Free PMC article.
Comparisons between different polychemotherapy regimens for early breast cancer: meta-analyses of long-term outcome among 100,000 women in 123 randomised trials.
Early Breast Cancer Trialists' Collaborative Group (EBCTCG), R Peto, +15 authors, K Pritchard.
Lancet, 2011 Dec 14; 379(9814). PMID: 22152853    Free PMC article.
Highly Cited.
Jetset: selecting the optimal microarray probe set to represent a gene.
Qiyuan Li, Nicolai J Birkbak, +2 authors, Aron C Eklund.
BMC Bioinformatics, 2011 Dec 17; 12. PMID: 22172014    Free PMC article.
Highly Cited.
Drug repositioning using disease associated biological processes and network analysis of drug targets.
Sachin Mathur, Deendayal Dinakarpandian.
AMIA Annu Symp Proc, 2011 Dec 24; 2011. PMID: 22195082    Free PMC article.
The influence of feature selection methods on accuracy, stability and interpretability of molecular signatures.
Anne-Claire Haury, Pierre Gestraud, Jean-Philippe Vert.
PLoS One, 2011 Dec 30; 6(12). PMID: 22205940    Free PMC article.
Luminal-B breast cancer and novel therapeutic targets.
Ben Tran, Philippe L Bedard.
Breast Cancer Res, 2012 Jan 06; 13(6). PMID: 22217398    Free PMC article.
Review.
Prognostic value of proliferation assay in the luminal, HER2-positive, and triple-negative biologic classes of breast cancer.
Mohammed A Aleskandarany, Andrew R Green, +5 authors, Emad A Rakha.
Breast Cancer Res, 2012 Jan 10; 14(1). PMID: 22225836    Free PMC article.
Integrated proteomic, transcriptomic, and biological network analysis of breast carcinoma reveals molecular features of tumorigenesis and clinical relapse.
Marcin Imielinski, Sangwon Cha, +3 authors, Dennis C Sgroi.
Mol Cell Proteomics, 2012 Jan 14; 11(6). PMID: 22240506    Free PMC article.
Robust rank aggregation for gene list integration and meta-analysis.
Raivo Kolde, Sven Laur, Priit Adler, Jaak Vilo.
Bioinformatics, 2012 Jan 17; 28(4). PMID: 22247279    Free PMC article.
Highly Cited.
Comprehensive literature review and statistical considerations for microarray meta-analysis.
George C Tseng, Debashis Ghosh, Eleanor Feingold.
Nucleic Acids Res, 2012 Jan 21; 40(9). PMID: 22262733    Free PMC article.
Highly Cited. Review.
A three-gene model to robustly identify breast cancer molecular subtypes.
Benjamin Haibe-Kains, Christine Desmedt, +4 authors, Christos Sotiriou.
J Natl Cancer Inst, 2012 Jan 21; 104(4). PMID: 22262870    Free PMC article.
Highly Cited.
A mammary stem cell population identified and characterized in late embryogenesis reveals similarities to human breast cancer.
Benjamin T Spike, Dannielle D Engle, +3 authors, Geoffrey M Wahl.
Cell Stem Cell, 2012 Feb 07; 10(2). PMID: 22305568    Free PMC article.
Highly Cited.
Mixed effects modeling of proliferation rates in cell-based models: consequence for pharmacogenomics and cancer.
Hae Kyung Im, Eric R Gamazon, +3 authors, M Eileen Dolan.
PLoS Genet, 2012 Feb 22; 8(2). PMID: 22346769    Free PMC article.
A phenotypic mouse model of basaloid breast tumors.
Soyoung Kim, Avtar Roopra, Caroline M Alexander.
PLoS One, 2012 Feb 22; 7(2). PMID: 22347416    Free PMC article.
A gene signature for predicting outcome in patients with basal-like breast cancer.
Robin M Hallett, Anna Dvorkin-Gheva, Anita Bane, John A Hassell.
Sci Rep, 2012 Feb 23; 2. PMID: 22355741    Free PMC article.
A prognostic gene expression profile that predicts circulating tumor cell presence in breast cancer patients.
Timothy J Molloy, Paul Roepman, Bjørn Naume, Laura J van't Veer.
PLoS One, 2012 Mar 03; 7(2). PMID: 22384245    Free PMC article.
Functional characterization of the 19q12 amplicon in grade III breast cancers.
Rachael Natrajan, Alan Mackay, +13 authors, Jorge S Reis-Filho.
Breast Cancer Res, 2012 Mar 22; 14(2). PMID: 22433433    Free PMC article.
Peritumoral vascular invasion and NHERF1 expression define an immunophenotype of grade 2 invasive breast cancer associated with poor prognosis.
Andrea Malfettone, Concetta Saponaro, +2 authors, Annita Mangia.
BMC Cancer, 2012 Mar 24; 12. PMID: 22439624    Free PMC article.
Respective prognostic value of genomic grade and histological proliferation markers in early stage (pN0) breast carcinoma.
Fabien Reyal, Marc A Bollet, +9 authors, Xavier Sastre-Garau.
PLoS One, 2012 Apr 25; 7(4). PMID: 22529987    Free PMC article.
Concordance among gene expression-based predictors for ER-positive breast cancer treated with adjuvant tamoxifen.
A Prat, J S Parker, +9 authors, C M Perou.
Ann Oncol, 2012 Apr 26; 23(11). PMID: 22532584    Free PMC article.
Aurora kinase A outperforms Ki67 as a prognostic marker in ER-positive breast cancer.
H R Ali, S-J Dawson, +3 authors, C Caldas.
Br J Cancer, 2012 Apr 28; 106(11). PMID: 22538974    Free PMC article.
A target based approach identifies genomic predictors of breast cancer patient response to chemotherapy.
Robin M Hallett, Gregory Pond, John A Hassell.
BMC Med Genomics, 2012 May 15; 5. PMID: 22578285    Free PMC article.
Adiposity, hormone replacement therapy use and breast cancer risk by age and hormone receptor status: a large prospective cohort study.
Rebecca Ritte, Annekatrin Lukanova, +44 authors, Rudolf Kaaks.
Breast Cancer Res, 2012 May 16; 14(3). PMID: 22583394    Free PMC article.
Comparison of data-merging methods with SVM attribute selection and classification in breast cancer gene expression.
Vitoantonio Bevilacqua, Paolo Pannarale, +3 authors, Stefania Tommasi.
BMC Bioinformatics, 2012 May 25; 13 Suppl 7. PMID: 22595006    Free PMC article.
Strategies for the discovery and development of therapies for metastatic breast cancer.
Bedrich L Eckhardt, Prudence A Francis, Belinda S Parker, Robin L Anderson.
Nat Rev Drug Discov, 2012 Jun 02; 11(6). PMID: 22653217
Highly Cited. Review.
Prognostic signatures in breast cancer: correlation does not imply causation.
Charlotte Ng, Britta Weigelt, Anita Grigoriadis, Jorge S Reis-Filho.
Breast Cancer Res, 2012 Jun 21; 14(3). PMID: 22713235    Free PMC article.
Stromal genes add prognostic information to proliferation and histoclinical markers: a basis for the next generation of breast cancer gene signatures.
Dwain Mefford, Joel Mefford.
PLoS One, 2012 Jun 22; 7(6). PMID: 22719844    Free PMC article.
Independent and functional validation of a multi-tumour-type proliferation signature.
M H W Starmans, N G Lieuwes, +8 authors, P Lambin.
Br J Cancer, 2012 Jun 23; 107(3). PMID: 22722312    Free PMC article.
Whole transcriptome RNA-Seq analysis of breast cancer recurrence risk using formalin-fixed paraffin-embedded tumor tissue.
Dominick Sinicropi, Kunbin Qu, +14 authors, Joffre Baker.
PLoS One, 2012 Jul 19; 7(7). PMID: 22808097    Free PMC article.
Prognostic molecular assays on the rise for non-small cell lung cancer.
William Sterlacci, Alexandar Tzankov.
J Thorac Dis, 2012 Jul 27; 4(2). PMID: 22833831    Free PMC article.
Breast cancer proteome takes more than two to tango on TRAIL: beat them at their own game.
Ammad Ahmad Farooqi, Sundas Fayyaz, +2 authors, Shahzad Bhatti.
J Membr Biol, 2012 Aug 18; 245(12). PMID: 22899350
Review.
Human epidermal growth factor receptor-2-positive breast cancer: does estrogen receptor status define two distinct subtypes?
I Vaz-Luis, E P Winer, N U Lin.
Ann Oncol, 2012 Oct 02; 24(2). PMID: 23022997    Free PMC article.
Review.
Expression of aurora kinase A is associated with metastasis-free survival in node-negative breast cancer patients.
Wulf Siggelkow, Daniel Boehm, +12 authors, Marcus Schmidt.
BMC Cancer, 2012 Nov 29; 12. PMID: 23186136    Free PMC article.
An array CGH based genomic instability index (G2I) is predictive of clinical outcome in breast cancer and reveals a subset of tumors without lymph node involvement but with poor prognosis.
Françoise Bonnet, Mickael Guedj, +14 authors, Michel Longy.
BMC Med Genomics, 2012 Nov 29; 5. PMID: 23186559    Free PMC article.
Basal/HER2 breast carcinomas: integrating molecular taxonomy with cancer stem cell dynamics to predict primary resistance to trastuzumab (Herceptin).
Begoña Martin-Castillo, Cristina Oliveras-Ferraros, +7 authors, Javier A Menendez.
Cell Cycle, 2012 Dec 21; 12(2). PMID: 23255137    Free PMC article.
bc-GenExMiner 3.0: new mining module computes breast cancer gene expression correlation analyses.
Pascal Jézéquel, Jean-Sébastien Frénel, +4 authors, Mario Campone.
Database (Oxford), 2013 Jan 18; 2013. PMID: 23325629    Free PMC article.
Utility of prognostic genomic tests in breast cancer practice: The IMPAKT 2012 Working Group Consensus Statement.
H A Azim, S Michiels, +9 authors, C Swanton.
Ann Oncol, 2013 Jan 23; 24(3). PMID: 23337633    Free PMC article.
Significance analysis of prognostic signatures.
Andrew H Beck, Nicholas W Knoblauch, +7 authors, Benjamin Haibe-Kains.
PLoS Comput Biol, 2013 Feb 01; 9(1). PMID: 23365551    Free PMC article.
A simple immunohistochemical panel comprising 2 conventional markers, Ki67 and p53, is a powerful tool for predicting patient outcome in luminal-type breast cancer.
Takayuki Kobayashi, Keiichi Iwaya, +4 authors, Osamu Matsubara.
BMC Clin Pathol, 2013 Feb 07; 13. PMID: 23384409    Free PMC article.
Inter-individual differences in response to dietary intervention: integrating omics platforms towards personalised dietary recommendations.
Johanna W Lampe, Sandi L Navarro, Meredith A J Hullar, Ali Shojaie.
Proc Nutr Soc, 2013 Feb 08; 72(2). PMID: 23388096    Free PMC article.
Neoplastic and stromal cells contribute to an extracellular matrix gene expression profile defining a breast cancer subtype likely to progress.
Tiziana Triulzi, Patrizia Casalini, +7 authors, Elda Tagliabue.
PLoS One, 2013 Feb 27; 8(2). PMID: 23441215    Free PMC article.
Embryonic mammary signature subsets are activated in Brca1-/- and basal-like breast cancers.
Marketa Zvelebil, Erik Oliemuller, +6 authors, Beatrice A Howard.
Breast Cancer Res, 2013 Mar 20; 15(2). PMID: 23506684    Free PMC article.
Gene expression profile analysis of t1 and t2 breast cancer reveals different activation pathways.
Margit L H Riis, Xi Zhao, +6 authors, Vessela N Kristensen.
ISRN Oncol, 2013 Mar 28; 2013. PMID: 23533813    Free PMC article.
Interactions between immunity, proliferation and molecular subtype in breast cancer prognosis.
Srikanth Nagalla, Jeff W Chou, +9 authors, Lance D Miller.
Genome Biol, 2013 Apr 27; 14(4). PMID: 23618380    Free PMC article.
Highly Cited.
Improving breast cancer survival analysis through competition-based multidimensional modeling.
Erhan Bilal, Janusz Dutkowski, +21 authors, Adam A Margolin.
PLoS Comput Biol, 2013 May 15; 9(5). PMID: 23671412    Free PMC article.
Ki-67 is a prognostic parameter in breast cancer patients: results of a large population-based cohort of a cancer registry.
E C Inwald, M Klinkhammer-Schalke, +4 authors, O Ortmann.
Breast Cancer Res Treat, 2013 May 16; 139(2). PMID: 23674192    Free PMC article.
Highly Cited.
Comprehensive analysis of correlation coefficients estimated from pooling heterogeneous microarray data.
Márcia M Almeida-de-Macedo, Nick Ransom, +2 authors, Eve Syrkin Wurtele.
BMC Bioinformatics, 2013 Jul 05; 14. PMID: 23822712    Free PMC article.
Gene expression patterns unveil a new level of molecular heterogeneity in colorectal cancer.
Eva Budinska, Vlad Popovici, +10 authors, Mauro Delorenzi.
J Pathol, 2013 Jul 10; 231(1). PMID: 23836465    Free PMC article.
Highly Cited.
Aberrant regulation of the BST2 (Tetherin) promoter enhances cell proliferation and apoptosis evasion in high grade breast cancer cells.
Aejaz Sayeed, Gloria Luciani-Torres, +3 authors, Shanaz H Dairkee.
PLoS One, 2013 Jul 11; 8(6). PMID: 23840623    Free PMC article.
Meta-analysis of microarray data identifies GAS6 expression as an independent predictor of poor survival in ovarian cancer.
Michelle Buehler, Brian Tse, +5 authors, Viola Heinzelmann-Schwarz.
Biomed Res Int, 2013 Jul 24; 2013. PMID: 23878800    Free PMC article.
Luminal breast cancer: from biology to treatment.
Michail Ignatiadis, Christos Sotiriou.
Nat Rev Clin Oncol, 2013 Jul 25; 10(9). PMID: 23881035
Review.
Are two-centimeter breast cancers large or small?
S A Narod, J Iqbal, +6 authors, J Lubinski.
Curr Oncol, 2013 Aug 02; 20(4). PMID: 23904761    Free PMC article.
Personalizing the treatment of women with early breast cancer: highlights of the St Gallen International Expert Consensus on the Primary Therapy of Early Breast Cancer 2013.
A Goldhirsch, E P Winer, +5 authors, Panel members.
Ann Oncol, 2013 Aug 07; 24(9). PMID: 23917950    Free PMC article.
Highly Cited.
Endothelial-like properties of claudin-low breast cancer cells promote tumor vascular permeability and metastasis.
J Chuck Harrell, Adam D Pfefferle, +7 authors, Charles M Perou.
Clin Exp Metastasis, 2013 Aug 27; 31(1). PMID: 23975155    Free PMC article.
Grading breast cancer tissues using molecular portraits.
Niclas Olsson, Petter Carlsson, +7 authors, Carl A K Borrebaeck.
Mol Cell Proteomics, 2013 Aug 29; 12(12). PMID: 23982162    Free PMC article.
A molecular signature predictive of indolent prostate cancer.
Shazia Irshad, Mukesh Bansal, +10 authors, Cory Abate-Shen.
Sci Transl Med, 2013 Sep 13; 5(202). PMID: 24027026    Free PMC article.
Prediction of late distant recurrence in patients with oestrogen-receptor-positive breast cancer: a prospective comparison of the breast-cancer index (BCI) assay, 21-gene recurrence score, and IHC4 in the TransATAC study population.
Dennis C Sgroi, Ivana Sestak, +9 authors, Mitch Dowsett.
Lancet Oncol, 2013 Sep 17; 14(11). PMID: 24035531    Free PMC article.
Highly Cited.
Validation of a proliferation-based expression signature as prognostic marker in early stage lung adenocarcinoma.
Ignacio I Wistuba, Carmen Behrens, +16 authors, Edward S Kim.
Clin Cancer Res, 2013 Sep 21; 19(22). PMID: 24048333    Free PMC article.
Tumor histological subtyping determined by hormone receptors and HER2 status defines different pathological complete response and outcome to dose-dense neoadjuvant chemotherapy in breast cancer patients.
A Sánchez-Muñoz, Y Plata-Fernández, +7 authors, P Sánchez-Rovira.
Clin Transl Oncol, 2013 Oct 03; 16(6). PMID: 24085576
Lymph node involvement in immunohistochemistry-based molecular classifications of breast cancer.
Nicholas K Howland, Teryn D Driver, +5 authors, Celia Chao.
J Surg Res, 2013 Oct 08; 185(2). PMID: 24095025    Free PMC article.
Hybrid method for prediction of metastasis in breast cancer patients using gene expression signals.
Alireza Mehri Dehnavi, Mohammad Reza Sehhati, Hossein Rabbani.
J Med Signals Sens, 2013 Oct 08; 3(2). PMID: 24098861    Free PMC article.
Breast tumors with elevated expression of 1q candidate genes confer poor clinical outcome and sensitivity to Ras/PI3K inhibition.
Muthulakshmi Muthuswami, Vignesh Ramesh, +6 authors, Kumaresan Ganesan.
PLoS One, 2013 Oct 23; 8(10). PMID: 24147022    Free PMC article.
Pattern of recurrence of early breast cancer is different according to intrinsic subtype and proliferation index.
Nuria Ribelles, Lidia Perez-Villa, +11 authors, Emilio Alba.
Breast Cancer Res, 2013 Oct 24; 15(5). PMID: 24148581    Free PMC article.
An optimized five-gene multi-platform predictor of hormone receptor negative and triple negative breast cancer metastatic risk.
Christina Yau, John Sninsky, +9 authors, Christopher C Benz.
Breast Cancer Res, 2013 Nov 01; 15(5). PMID: 24172169    Free PMC article.
Biomarkers for Basal-like Breast Cancer.
Jennifer R Choo, Torsten O Nielsen.
Cancers (Basel), 2010 Jan 01; 2(2). PMID: 24281106    Free PMC article.
Reproductive factors and risk of hormone receptor positive and negative breast cancer: a cohort study.
Rebecca Ritte, Kaja Tikk, +41 authors, Rudolf Kaaks.
BMC Cancer, 2013 Dec 11; 13. PMID: 24321460    Free PMC article.
The prognostic value of mitotic activity index (MAI), phosphohistone H3 (PPH3), cyclin B1, cyclin A, and Ki67, alone and in combinations, in node-negative premenopausal breast cancer.
Marie Klintman, Carina Strand, +11 authors, Mårten Fernö.
PLoS One, 2013 Dec 11; 8(12). PMID: 24324728    Free PMC article.
A comparative analysis of biomarker selection techniques.
Nicoletta Dessì, Emanuele Pascariello, Barbara Pes.
Biomed Res Int, 2013 Dec 11; 2013. PMID: 24324960    Free PMC article.
A prognostic gene signature for metastasis-free survival of triple negative breast cancer patients.
Unjin Lee, Casey Frankenberger, +6 authors, Marsha Rich Rosner.
PLoS One, 2013 Dec 19; 8(12). PMID: 24349199    Free PMC article.
Overview of diagnostic/targeted treatment combinations in personalized medicine for breast cancer patients.
Anna Tessari, Dario Palmieri, Serena Di Cosimo.
Pharmgenomics Pers Med, 2014 Jan 10; 7. PMID: 24403841    Free PMC article.
Review.
Combined analysis of chromosomal instabilities and gene expression for colon cancer progression inference.
Claudia Cava, Italo Zoppis, +3 authors, Marco Antoniotti.
J Clin Bioinforma, 2014 Jan 25; 4(1). PMID: 24456927    Free PMC article.
Gene co-expression modules as clinically relevant hallmarks of breast cancer diversity.
Denise M Wolf, Marc E Lenburg, +2 authors, Laura J van 't Veer.
PLoS One, 2014 Feb 12; 9(2). PMID: 24516633    Free PMC article.
Genomic profiling in luminal breast cancer.
Oleg Gluz, Daniel Hofmann, +3 authors, Nadia Harbeck.
Breast Care (Basel), 2014 Feb 20; 8(6). PMID: 24550749    Free PMC article.
Review.
Annotation enrichment analysis: an alternative method for evaluating the functional properties of gene sets.
Kimberly Glass, Michelle Girvan.
Sci Rep, 2014 Feb 27; 4. PMID: 24569707    Free PMC article.
Gene expression analysis in RA: towards personalized medicine.
A N Burska, K Roget, +8 authors, F Ponchel.
Pharmacogenomics J, 2014 Mar 05; 14(2). PMID: 24589910    Free PMC article.
Review.
Prognostic value of gene signatures and proliferation in lymph-node-negative breast cancer.
Kristin Jonsdottir, Jörg Assmus, +4 authors, Emiel A M Janssen.
PLoS One, 2014 Mar 07; 9(3). PMID: 24599057    Free PMC article.
Relationship of CK8/18 expression pattern to breast cancer immunohistochemical subtyping in Egyptian patients.
Hayam A Aiad, Rehab M Samaka, +3 authors, Islam M Miligy.
Ecancermedicalscience, 2014 Mar 08; 8. PMID: 24605136    Free PMC article.
Baseline staging tests based on molecular subtype is necessary for newly diagnosed breast cancer.
Xuesong Chen, Lichun Sun, +8 authors, Xiaoqun Dong.
J Exp Clin Cancer Res, 2014 Mar 19; 33. PMID: 24628817    Free PMC article.
Multi-level gene expression signatures, but not binary, outperform Ki67 for the long term prognostication of breast cancer patients.
Nicholas P Tobin, Linda S Lindström, +3 authors, Kristian Wennmalm.
Mol Oncol, 2014 Mar 19; 8(3). PMID: 24630985    Free PMC article.
Systematic assessment of prognostic gene signatures for breast cancer shows distinct influence of time and ER status.
Xi Zhao, Einar Andreas Rødland, +5 authors, Anne-Lise Børresen-Dale.
BMC Cancer, 2014 Mar 22; 14. PMID: 24645668    Free PMC article.
Estrogen receptor-positive breast cancer molecular signatures and therapeutic potentials (Review).
Mei Hong Zhang, Hong Tao Man, +2 authors, Shi Liang Ma.
Biomed Rep, 2014 Mar 22; 2(1). PMID: 24649067    Free PMC article.
Predictive performance of microarray gene signatures: impact of tumor heterogeneity and multiple mechanisms of drug resistance.
Charlotte K Y Ng, Britta Weigelt, +5 authors, Jorge S Reis-Filho.
Cancer Res, 2014 Apr 08; 74(11). PMID: 24706696    Free PMC article.
Multigene Assays for Classification, Prognosis, and Prediction in Breast Cancer: a Critical Review on the Background and Clinical Utility.
P Sinn, S Aulmann, +6 authors, A Schneeweiss.
Geburtshilfe Frauenheilkd, 2014 Apr 29; 73(9). PMID: 24771945    Free PMC article.
Fifteen years SIB Swiss Institute of Bioinformatics: life science databases, tools and support.
Heinz Stockinger, Adrian M Altenhoff, +21 authors, Ron D Appel.
Nucleic Acids Res, 2014 May 06; 42(Web Server issue). PMID: 24792157    Free PMC article.
Chromatin CKAP2, a new proliferation marker, as independent prognostic indicator in breast cancer.
Han-Seong Kim, Jae-Soo Koh, +12 authors, Kyeong-Man Hong.
PLoS One, 2014 Jun 03; 9(6). PMID: 24887265    Free PMC article.
Tumor microenvironment of metastasis and risk of distant metastasis of breast cancer.
Thomas E Rohan, Xiaonan Xue, +10 authors, Joan G Jones.
J Natl Cancer Inst, 2014 Jun 05; 106(8). PMID: 24895374    Free PMC article.
Highly Cited.
Luminal breast cancer classification according to proliferative indices: clinicopathological characteristics and short-term survival analysis.
Yan Sun, Gang Nie, +3 authors, Haibo Wang.
Med Oncol, 2014 Jun 18; 31(7). PMID: 24935624
Decreased expression of C10orf10 and its prognostic significance in human breast cancer.
Junjiang Deng, Yan Dong, +4 authors, Jianjun Li.
PLoS One, 2014 Jun 18; 9(6). PMID: 24936657    Free PMC article.
A prognostic model of triple-negative breast cancer based on miR-27b-3p and node status.
Songjie Shen, Qiang Sun, +5 authors, Yidong Zhou.
PLoS One, 2014 Jun 20; 9(6). PMID: 24945253    Free PMC article.
Proposed new clinicopathological surrogate definitions of luminal A and luminal B (HER2-negative) intrinsic breast cancer subtypes.
Patrick Maisonneuve, Davide Disalvatore, +10 authors, Aron Goldhirsch.
Breast Cancer Res, 2014 Jun 22; 16(3). PMID: 24951027    Free PMC article.
Chromosomal instability selects gene copy-number variants encoding core regulators of proliferation in ER+ breast cancer.
David Endesfelder, Rebecca Burrell, +6 authors, Maik Kschischo.
Cancer Res, 2014 Jun 28; 74(17). PMID: 24970479    Free PMC article.
Temporal gene expression analysis of Sjögren's syndrome in C57BL/6.NOD-Aec1Aec2 mice based on microarray time-series data using an improved empirical Bayes approach.
Dan Wang, Luan Xue, +3 authors, Xuemei Piao.
Mol Biol Rep, 2014 Jul 06; 41(9). PMID: 24990690
Biological subtypes of breast cancer: Prognostic and therapeutic implications.
Ozlem Yersal, Sabri Barutca.
World J Clin Oncol, 2014 Aug 13; 5(3). PMID: 25114856    Free PMC article.
Highly Cited. Review.
How many etiological subtypes of breast cancer: two, three, four, or more?
William F Anderson, Philip S Rosenberg, +2 authors, Mark E Sherman.
J Natl Cancer Inst, 2014 Aug 15; 106(8). PMID: 25118203    Free PMC article.
Highly Cited. Review.
An integrated genomics approach identifies drivers of proliferation in luminal-subtype human breast cancer.
Michael L Gatza, Grace O Silva, +2 authors, Charles M Perou.
Nat Genet, 2014 Aug 26; 46(10). PMID: 25151356    Free PMC article.
Highly Cited.
Genome-driven integrated classification of breast cancer validated in over 7,500 samples.
H Raza Ali, Oscar M Rueda, +4 authors, Carlos Caldas.
Genome Biol, 2014 Aug 29; 15(8). PMID: 25164602    Free PMC article.
Highly Cited.
Weibull regression with Bayesian variable selection to identify prognostic tumour markers of breast cancer survival.
P J Newcombe, H Raza Ali, +4 authors, S Richardson.
Stat Methods Med Res, 2014 Sep 07; 26(1). PMID: 25193065    Free PMC article.
Molecular breast cancer subtypes and therapies in a public hospital of northeastern Brazil.
Ana Cláudia de Macêdo Andrade, Carlos Alberis Ferreira Júnior, +3 authors, Mathias Weller.
BMC Womens Health, 2014 Sep 14; 14. PMID: 25216732    Free PMC article.
Immunohistochemical detection improves the prognostic value of lymphatic and blood vessel invasion in primary ductal breast cancer.
Fadia J A Gujam, James J Going, +3 authors, Donald C McMillan.
BMC Cancer, 2014 Sep 23; 14. PMID: 25234410    Free PMC article.
Integrative clustering methods for high-dimensional molecular data.
Prabhakar Chalise, Devin C Koestler, +2 authors, Brooke L Fridley.
Transl Cancer Res, 2014 Sep 23; 3(3). PMID: 25243110    Free PMC article.
Integrative analysis of cancer imaging readouts by networks.
Marco Dominietto, Nicholas Tsinoremas, Enrico Capobianco.
Mol Oncol, 2014 Sep 30; 9(1). PMID: 25263240    Free PMC article.
Review.
Association between molecular subtypes and lymph node status in invasive breast cancer.
Chengshuai Si, Yiting Jin, Hongying Wang, Qiang Zou.
Int J Clin Exp Pathol, 2014 Nov 18; 7(10). PMID: 25400761    Free PMC article.
Transfer of clinically relevant gene expression signatures in breast cancer: from Affymetrix microarray to Illumina RNA-Sequencing technology.
Debora Fumagalli, Alexis Blanchet-Cohen, +13 authors, Benjamin Haibe-Kains.
BMC Genomics, 2014 Nov 22; 15. PMID: 25412710    Free PMC article.
The histone chaperone HJURP is a new independent prognostic marker for luminal A breast carcinoma.
Rocío Montes de Oca, Zachary A Gurard-Levin, +12 authors, Geneviève Almouzni.
Mol Oncol, 2014 Dec 17; 9(3). PMID: 25497280    Free PMC article.
Standardized uptake value of ¹⁸F-fluorodeoxyglucose positron emission tomography for prediction of tumor recurrence in breast cancer beyond tumor burden.
Sung Gwe Ahn, Jong Tae Park, +8 authors, Joon Jeong.
Breast Cancer Res, 2015 Jan 01; 16(6). PMID: 25551703    Free PMC article.
Clinical and histopathological factors associated with Ki-67 expression in breast cancer patients.
Gul Alco, Atilla Bozdogan, +8 authors, Vahit Ozmen.
Oncol Lett, 2015 Feb 11; 9(3). PMID: 25663855    Free PMC article.
Treatment-induced cell cycle kinetics dictate tumor response to chemotherapy.
Robin M Hallett, Cheng Huang, +5 authors, Jonathan S Draper.
Oncotarget, 2015 Mar 10; 6(9). PMID: 25749523    Free PMC article.
Network-based approach to identify prognostic biomarkers for estrogen receptor-positive breast cancer treatment with tamoxifen.
Rong Liu, Cheng-Xian Guo, Hong-Hao Zhou.
Cancer Biol Ther, 2015 Mar 11; 16(2). PMID: 25756514    Free PMC article.
Strong adverse effect of epidermal growth factor receptor 2 overexpression on prognosis of patients with invasive lobular breast cancer: a comparative study with invasive ductal breast cancer in Chinese population.
Tong Wang, Yuanyuan Ma, +3 authors, Ruifang Niu.
Tumour Biol, 2015 Mar 26; 36(8). PMID: 25804795
Robust meta-analysis of gene expression using the elastic net.
Jacob J Hughey, Atul J Butte.
Nucleic Acids Res, 2015 Apr 02; 43(12). PMID: 25829177    Free PMC article.
Evaluation of public cancer datasets and signatures identifies TP53 mutant signatures with robust prognostic and predictive value.
Brian David Lehmann, Yan Ding, +6 authors, Yajun Yi.
BMC Cancer, 2015 Apr 18; 15. PMID: 25886164    Free PMC article.
Long non-coding RNA expression profiles predict metastasis in lymph node-negative breast cancer independently of traditional prognostic markers.
Kristina P Sørensen, Mads Thomassen, +5 authors, Torben A Kruse.
Breast Cancer Res, 2015 Apr 19; 17. PMID: 25887545    Free PMC article.
Fuzzy logic selection as a new reliable tool to identify molecular grade signatures in breast cancer--the INNODIAG study.
Tatiana Kempowsky-Hamon, Carine Valle, +12 authors, Véronique Anton-Leberre.
BMC Med Genomics, 2015 Apr 19; 8. PMID: 25888889    Free PMC article.
Molecular characterization and targeted therapeutic approaches in breast cancer.
Angela Toss, Massimo Cristofanilli.
Breast Cancer Res, 2015 Apr 24; 17. PMID: 25902832    Free PMC article.
Review.
Combined Proteomics and Transcriptomics Identifies Carboxypeptidase B1 and Nuclear Factor κB (NF-κB) Associated Proteins as Putative Biomarkers of Metastasis in Low Grade Breast Cancer.
Pavel Bouchal, Monika Dvořáková, +11 authors, Rudolf Nenutil.
Mol Cell Proteomics, 2015 Apr 24; 14(7). PMID: 25903579    Free PMC article.
Five-year risk of interval-invasive second breast cancer.
Janie M Lee, Diana S M Buist, +6 authors, Rebecca A Hubbard.
J Natl Cancer Inst, 2015 Apr 24; 107(7). PMID: 25904721    Free PMC article.
Tailoring therapies--improving the management of early breast cancer: St Gallen International Expert Consensus on the Primary Therapy of Early Breast Cancer 2015.
A S Coates, E P Winer, +6 authors, Panel Members.
Ann Oncol, 2015 May 06; 26(8). PMID: 25939896    Free PMC article.
Highly Cited.
Identification and evaluation of network modules for the prognosis of basal-like breast cancer.
Robin M Hallett, Jessica G Cockburn, +3 authors, Anita Bane.
Oncotarget, 2015 May 21; 6(19). PMID: 25991675    Free PMC article.
Association of Protein Translation and Extracellular Matrix Gene Sets with Breast Cancer Metastasis: Findings Uncovered on Analysis of Multiple Publicly Available Datasets Using Individual Patient Data Approach.
Nilotpal Chowdhury, Shantanu Sapru.
PLoS One, 2015 Jun 17; 10(6). PMID: 26080057    Free PMC article.
An integrated approach to reveal miRNAs' impacts on the functional consequence of copy number alterations in cancer.
Kening Li, Yongjing Liu, +7 authors, Yan Xu.
Sci Rep, 2015 Jun 24; 5. PMID: 26099552    Free PMC article.
CIB1 depletion impairs cell survival and tumor growth in triple-negative breast cancer.
Justin L Black, J Chuck Harrell, +8 authors, Leslie V Parise.
Breast Cancer Res Treat, 2015 Jun 25; 152(2). PMID: 26105795    Free PMC article.
A reproducible approach to high-throughput biological data acquisition and integration.
Daniela Börnigen, Yo Sup Moon, +9 authors, Curtis Huttenhower.
PeerJ, 2015 Jul 15; 3. PMID: 26157642    Free PMC article.
Evaluation of an Optimal Cut-Off Point for the Ki-67 Index as a Prognostic Factor in Primary Breast Cancer: A Retrospective Study.
Rumiko Tashima, Reiki Nishimura, +6 authors, Nobuyuki Arima.
PLoS One, 2015 Jul 16; 10(7). PMID: 26177501    Free PMC article.
Systems biology approach to studying proliferation-dependent prognostic subnetworks in breast cancer.
Qianqian Song, Hongyan Wang, +4 authors, Xiaobo Zhou.
Sci Rep, 2015 Aug 11; 5. PMID: 26257336    Free PMC article.
Clinical Significance of Microcalcifications Detection in Invasive Breast Carcinoma.
Yuki Hashimoto, Aya Murata, +8 authors, Yasuaki Hirooka.
Yonago Acta Med, 2015 Aug 26; 58(2). PMID: 26306060    Free PMC article.
Comparing the performance of biomedical clustering methods.
Christian Wiwie, Jan Baumbach, Richard Röttger.
Nat Methods, 2015 Sep 22; 12(11). PMID: 26389570
RNA Enrichment Method for Quantitative Transcriptional Analysis of Pathogens In Vivo Applied to the Fungus Candida albicans.
Sara Amorim-Vaz, Van Du T Tran, +3 authors, Dominique Sanglard.
mBio, 2015 Sep 24; 6(5). PMID: 26396240    Free PMC article.
The relationship between quantitative human epidermal growth factor receptor 2 gene expression by the 21-gene reverse transcriptase polymerase chain reaction assay and adjuvant trastuzumab benefit in Alliance N9831.
Edith A Perez, Frederick L Baehner, +11 authors, Karla V Ballman.
Breast Cancer Res, 2015 Oct 03; 17(1). PMID: 26429296    Free PMC article.
Comparative study of joint analysis of microarray gene expression data in survival prediction and risk assessment of breast cancer patients.
Haleh Yasrebi.
Brief Bioinform, 2015 Oct 28; 17(5). PMID: 26504096    Free PMC article.
Sex Differences in Plasmacytoid Dendritic Cell Levels of IRF5 Drive Higher IFN-α Production in Women.
Morgane Griesbeck, Susanne Ziegler, +21 authors, Marcus Altfeld.
J Immunol, 2015 Nov 01; 195(11). PMID: 26519527    Free PMC article.
ADRA2A Germline Gene Polymorphism is Associated to the Severity, but not to the Risk, of Breast Cancer.
Batoul Kaabi, Ghania Belaaloui, +4 authors, Hocine Bounecer.
Pathol Oncol Res, 2015 Nov 14; 22(2). PMID: 26563278
Gene-expression signature functional annotation of breast cancer tumours in function of age.
Pascal Jézéquel, Zein Sharif, +5 authors, Mario Campone.
BMC Med Genomics, 2015 Nov 26; 8. PMID: 26597277    Free PMC article.
Cost-Utility of a Prognostic Test Guiding Adjuvant Chemotherapy Decisions in Early-Stage Non-Small Cell Lung Cancer.
David D Stenehjem, Brandon K Bellows, +4 authors, Diana I Brixner.
Oncologist, 2015 Nov 29; 21(2). PMID: 26614710    Free PMC article.
Gene signature combinations improve prognostic stratification of multiple myeloma patients.
W J Chng, T-H Chung, +6 authors, P Sonneveld.
Leukemia, 2015 Dec 17; 30(5). PMID: 26669975
Breast cancer intrinsic subtype classification, clinical use and future trends.
Xiaofeng Dai, Ting Li, +4 authors, Bozhi Shi.
Am J Cancer Res, 2015 Dec 23; 5(10). PMID: 26693050    Free PMC article.
Highly Cited. Review.
High Proliferation Predicts Pathological Complete Response to Neoadjuvant Chemotherapy in Early Breast Cancer.
Emilio Alba, Ana Lluch, +18 authors, Federico Rojo.
Oncologist, 2016 Jan 21; 21(2). PMID: 26786263    Free PMC article.
Estrogen-Receptor, Progesterone-Receptor and HER2 Status Determination in Invasive Breast Cancer. Concordance between Immuno-Histochemistry and MapQuant™ Microarray Based Assay.
D Mouttet, M Laé, +8 authors, F Reyal.
PLoS One, 2016 Feb 02; 11(2). PMID: 26829108    Free PMC article.
Low Concordance between Gene Expression Signatures in ER Positive HER2 Negative Breast Carcinoma Could Impair Their Clinical Application.
Enora Laas, Peter Mallon, +3 authors, Fabien Reyal.
PLoS One, 2016 Feb 20; 11(2). PMID: 26895349    Free PMC article.
A Model-Based Joint Identification of Differentially Expressed Genes and Phenotype-Associated Genes.
Samuel Sunghwan Cho, Yongkang Kim, +9 authors, Taesung Park.
PLoS One, 2016 Mar 11; 11(3). PMID: 26964035    Free PMC article.
Absolute Benefit of Adjuvant Endocrine Therapies for Premenopausal Women With Hormone Receptor-Positive, Human Epidermal Growth Factor Receptor 2-Negative Early Breast Cancer: TEXT and SOFT Trials.
Meredith M Regan, Prudence A Francis, +12 authors, Richard D Gelber.
J Clin Oncol, 2016 Apr 06; 34(19). PMID: 27044936    Free PMC article.
Signatures of breast cancer metastasis at a glance.
George S Karagiannis, Sumanta Goswami, +2 authors, John S Condeelis.
J Cell Sci, 2016 Apr 17; 129(9). PMID: 27084578    Free PMC article.
Review.
Testing chemotherapy efficacy in HER2 negative breast cancer using patient-derived spheroids.
Kathrin Halfter, Oliver Hoffmann, +6 authors, Barbara Mayer.
J Transl Med, 2016 May 05; 14(1). PMID: 27142386    Free PMC article.
Breast cancer subtype predictors revisited: from consensus to concordance?
Herman M J Sontrop, Marcel J T Reinders, Perry D Moerland.
BMC Med Genomics, 2016 Jun 05; 9(1). PMID: 27259591    Free PMC article.
The Role of Proliferation in Determining Response to Neoadjuvant Chemotherapy in Breast Cancer: A Gene Expression-Based Meta-Analysis.
Daniel G Stover, Jonathan L Coloff, +3 authors, Laura M Selfors.
Clin Cancer Res, 2016 Jun 23; 22(24). PMID: 27330058    Free PMC article.
Meta-analytic framework for sparse K-means to identify disease subtypes in multiple transcriptomic studies.
Zhiguang Huo, Ying Ding, +2 authors, George Tseng.
J Am Stat Assoc, 2016 Jun 23; 111(513). PMID: 27330233    Free PMC article.
Extensive Transcriptomic and Genomic Analysis Provides New Insights about Luminal Breast Cancers.
Inna Tishchenko, Heloisa Helena Milioli, Carlos Riveros, Pablo Moscato.
PLoS One, 2016 Jun 25; 11(6). PMID: 27341628    Free PMC article.
Cancer Hallmarks, Biomarkers and Breast Cancer Molecular Subtypes.
Xiaofeng Dai, Liangjian Xiang, Ting Li, Zhonghu Bai.
J Cancer, 2016 Jul 09; 7(10). PMID: 27390604    Free PMC article.
Highly Cited. Review.
Identification of novel biomarkers associated with poor patient outcomes in invasive breast carcinoma.
Renata A Canevari, Fabio A Marchi, +5 authors, Eduardo M Reis.
Tumour Biol, 2016 Aug 04; 37(10). PMID: 27485113
Classical pathology and mutational load of breast cancer - integration of two worlds.
Jan Budczies, Michael Bockmayr, +7 authors, Albrecht Stenzinger.
J Pathol Clin Res, 2016 Aug 09; 1(4). PMID: 27499907    Free PMC article.
Prognostic Value of a BCSC-associated MicroRNA Signature in Hormone Receptor-Positive HER2-Negative Breast Cancer.
Chang Gong, Weige Tan, +16 authors, Erwei Song.
EBioMedicine, 2016 Aug 28; 11. PMID: 27566954    Free PMC article.
Breast cancer classification and prognostication through diverse systems along with recent emerging findings in this respect; the dawn of new perspectives in the clinical applications.
Vida Pourteimoor, Samira Mohammadi-Yeganeh, Mahdi Paryan.
Tumour Biol, 2016 Sep 22; 37(11). PMID: 27651157
Review.
Drug Repositioning through Systematic Mining of Gene Coexpression Networks in Cancer.
Alexander E Ivliev, Peter A C 't Hoen, +2 authors, Marina G Sergeeva.
PLoS One, 2016 Nov 09; 11(11). PMID: 27824868    Free PMC article.
The molecular basis of breast cancer pathological phenotypes.
Yujing J Heng, Susan C Lester, +26 authors, Andrew H Beck.
J Pathol, 2016 Nov 20; 241(3). PMID: 27861902    Free PMC article.
MICRORNA-AUGMENTED PATHWAYS (mirAP) AND THEIR APPLICATIONS TO PATHWAY ANALYSIS AND DISEASE SUBTYPING.
Diana Diaz, Michele Donato, Tin Nguyen, Sorin Draghici.
Pac Symp Biocomput, 2016 Nov 30; 22. PMID: 27896992    Free PMC article.
Androgen Receptor: A Complex Therapeutic Target for Breast Cancer.
Ramesh Narayanan, James T Dalton.
Cancers (Basel), 2016 Dec 06; 8(12). PMID: 27918430    Free PMC article.
Review.
Harnessing benefit from targeting tumor associated carbohydrate antigens.
Thomas Kieber-Emmons, Behjatolah Monzavi-Karbassi, +2 authors, Issam Makhoul.
Hum Vaccin Immunother, 2016 Dec 09; 13(2). PMID: 27929800    Free PMC article.
Review.
Buformin inhibits the stemness of erbB-2-overexpressing breast cancer cells and premalignant mammary tissues of MMTV-erbB-2 transgenic mice.
Amanda B Parris, Qingxia Zhao, +3 authors, Xiaohe Yang.
J Exp Clin Cancer Res, 2017 Feb 15; 36(1). PMID: 28193239    Free PMC article.
Detecting gene signature activation in breast cancer in an absolute, single-patient manner.
E R Paquet, R Lesurf, +2 authors, M T Hallett.
Breast Cancer Res, 2017 Mar 23; 19(1). PMID: 28327201    Free PMC article.
Low Recombination Proficiency Score (RPS) Predicts Heightened Sensitivity to DNA-Damaging Chemotherapy in Breast Cancer.
Sean P Pitroda, Riyue Bao, +2 authors, Philip P Connell.
Clin Cancer Res, 2017 Mar 28; 23(15). PMID: 28341751    Free PMC article.
Comparison of standardized uptake value of 18F-FDG-PET-CT with 21-gene recurrence score in estrogen receptor-positive, HER2-negative breast cancer.
Sung Gwe Ahn, Jae-Hoon Lee, +8 authors, Seung Il Kim.
PLoS One, 2017 Apr 19; 12(4). PMID: 28419166    Free PMC article.
Single-cell RNA-seq enables comprehensive tumour and immune cell profiling in primary breast cancer.
Woosung Chung, Hye Hyeon Eum, +10 authors, Woong-Yang Park.
Nat Commun, 2017 May 06; 8. PMID: 28474673    Free PMC article.
Highly Cited.
Study of Meta-analysis strategies for network inference using information-theoretic approaches.
Ngoc C Pham, Benjamin Haibe-Kains, +2 authors, Patrick E Meyer.
BioData Min, 2017 May 10; 10. PMID: 28484519    Free PMC article.
Associating transcriptional modules with colon cancer survival through weighted gene co-expression network analysis.
Rong Liu, Wei Zhang, Zhao-Qian Liu, Hong-Hao Zhou.
BMC Genomics, 2017 May 11; 18(1). PMID: 28486948    Free PMC article.
An imprinted non-coding genomic cluster at 14q32 defines clinically relevant molecular subtypes in osteosarcoma across multiple independent datasets.
Katherine E Hill, Andrew D Kelly, +16 authors, Dimitrios Spentzos.
J Hematol Oncol, 2017 May 17; 10(1). PMID: 28506242    Free PMC article.
Clinical utility of gene-expression signatures in early stage breast cancer.
Maryann Kwa, Andreas Makris, Francisco J Esteva.
Nat Rev Clin Oncol, 2017 Jun 01; 14(10). PMID: 28561071
Highly Cited. Review.
The olive oil phenolic (-)-oleocanthal modulates estrogen receptor expression in luminal breast cancer in vitro and in vivo and synergizes with tamoxifen treatment.
Nehad M Ayoub, Abu Bakar Siddique, +2 authors, Khalid A El Sayed.
Eur J Pharmacol, 2017 Jun 20; 810. PMID: 28625568    Free PMC article.
Integrative analysis of copy number and gene expression in breast cancer using formalin-fixed paraffin-embedded core biopsy tissue: a feasibility study.
Mahesh Iddawela, Oscar Rueda, +4 authors, Carlos Caldas.
BMC Genomics, 2017 Jul 13; 18(1). PMID: 28697743    Free PMC article.
A multifactorial 'Consensus Signature' by in silico analysis to predict response to neoadjuvant anthracycline-based chemotherapy in triple-negative breast cancer.
Natalie Turner, Mattia Forcato, +3 authors, Angelo Di Leo.
NPJ Breast Cancer, 2015 Jun 02; 1. PMID: 28721363    Free PMC article.
The molecular landscape of high-risk early breast cancer: comprehensive biomarker analysis of a phase III adjuvant population.
Timothy R Wilson, Jianjun Yu, +17 authors, Mark R Lackner.
NPJ Breast Cancer, 2017 Jul 20; 2. PMID: 28721382    Free PMC article.
Triple-negative breast cancer: the importance of molecular and histologic subtyping, and recognition of low-grade variants.
Fresia Pareja, Felipe C Geyer, +3 authors, Jorge S Reis-Filho.
NPJ Breast Cancer, 2017 Jul 20; 2. PMID: 28721389    Free PMC article.
Highly Cited. Review.
Extracting replicable associations across multiple studies: Empirical Bayes algorithms for controlling the false discovery rate.
David Amar, Ron Shamir, Daniel Yekutieli.
PLoS Comput Biol, 2017 Aug 19; 13(8). PMID: 28821015    Free PMC article.
Epigenetic Mechanisms of Tamoxifen Resistance in Luminal Breast Cancer.
Hany A Abdel-Hafiz.
Diseases, 2017 Sep 22; 5(3). PMID: 28933369    Free PMC article.
Review.
Magnetic resonance metabolic profiling of estrogen receptor-positive breast cancer: correlation with currently used molecular markers.
Ji Soo Choi, Dahye Yoon, +5 authors, Min Jung Kim.
Oncotarget, 2017 Oct 04; 8(38). PMID: 28969000    Free PMC article.
Prognostic immune-related gene models for breast cancer: a pooled analysis.
Jianli Zhao, Ying Wang, +6 authors, Kai Chen.
Onco Targets Ther, 2017 Oct 06; 10. PMID: 28979134    Free PMC article.
Comparison of breast-conserving surgery with mastectomy in locally advanced breast cancer after good response to neoadjuvant chemotherapy: A PRISMA-compliant systematic review and meta-analysis.
Yixuan Sun, Mingjuan Liao, Liu He, Chenfang Zhu.
Medicine (Baltimore), 2017 Oct 27; 96(43). PMID: 29069026    Free PMC article.
Systematic Review.
Molecular Subtypes and Local-Regional Control of Breast Cancer.
Simona Maria Fragomeni, Andrew Sciallis, Jacqueline S Jeruss.
Surg Oncol Clin N Am, 2017 Nov 15; 27(1). PMID: 29132568    Free PMC article.
Review.
A metastasis biomarker (MetaSite Breast™ Score) is associated with distant recurrence in hormone receptor-positive, HER2-negative early-stage breast cancer.
Joseph A Sparano, Robert Gray, +13 authors, Joan Jones.
NPJ Breast Cancer, 2017 Nov 16; 3. PMID: 29138761    Free PMC article.
Adjuvant chemotherapeutic treatment of 1650 patients with early breast cancer in routine care in Germany: data from the prospective TMK cohort study.
Steffen Dörfel, Claus-Christoph Steffens, +6 authors, TMK-Group (Tumour Registry Breast Cancer).
Breast Cancer, 2017 Dec 06; 25(3). PMID: 29204847    Free PMC article.
Identification of cancer genes that are independent of dominant proliferation and lineage programs.
Laura M Selfors, Daniel G Stover, +2 authors, Jonathan L Coloff.
Proc Natl Acad Sci U S A, 2017 Dec 13; 114(52). PMID: 29229826    Free PMC article.
Tumor Heterogeneity in Breast Cancer.
Gulisa Turashvili, Edi Brogi.
Front Med (Lausanne), 2017 Dec 26; 4. PMID: 29276709    Free PMC article.
Highly Cited. Review.
De novo metastasis in breast cancer: occurrence and overall survival stratified by molecular subtype.
David J Press, Megan E Miller, +2 authors, Dezheng Huo.
Clin Exp Metastasis, 2017 Dec 31; 34(8). PMID: 29288366
Effects of rat bone marrow-derived mesenchymal stem cells on breast cancer cells with differing hormone receptor status.
Ying Wang, Shan Shao, +6 authors, Xinhan Zhao.
Oncol Lett, 2018 Jan 19; 14(6). PMID: 29344162    Free PMC article.
Shrinkage Clustering: a fast and size-constrained clustering algorithm for biomedical applications.
Chenyue W Hu, Hanyang Li, Amina A Qutub.
BMC Bioinformatics, 2018 Jan 25; 19(1). PMID: 29361928    Free PMC article.
Comparison of the Performance of 6 Prognostic Signatures for Estrogen Receptor-Positive Breast Cancer: A Secondary Analysis of a Randomized Clinical Trial.
Ivana Sestak, Richard Buus, +9 authors, Mitch Dowsett.
JAMA Oncol, 2018 Feb 17; 4(4). PMID: 29450494    Free PMC article.
Highly Cited.
New tools for old drugs: Functional genetic screens to optimize current chemotherapy.
Nora M Gerhards, Sven Rottenberg.
Drug Resist Updat, 2018 Mar 04; 36. PMID: 29499836    Free PMC article.
Review.
Guiding biomedical clustering with ClustEval.
Christian Wiwie, Jan Baumbach, Richard Röttger.
Nat Protoc, 2018 May 31; 13(6). PMID: 29844526
Prognostic gene expression assays in breast cancer: are two better than one?
Joseph A Sparano.
NPJ Breast Cancer, 2018 May 31; 4. PMID: 29845110    Free PMC article.
Correlation between minimum apparent diffusion coefficient values and the histological grade of breast invasive ductal carcinoma.
Suhong Zhao, Weihua Guo, +4 authors, Guangrui Shao.
Oncol Lett, 2018 Jun 01; 15(5). PMID: 29849809    Free PMC article.
Precision Medicine for Breast Cancer: The Paths to Truly Individualized Diagnosis and Treatment.
Eleanor E R Harris.
Int J Breast Cancer, 2018 Jun 05; 2018. PMID: 29862084    Free PMC article.
Review.
FGFR1 underlies obesity-associated progression of estrogen receptor-positive breast cancer after estrogen deprivation.
Elizabeth A Wellberg, Peter Kabos, +16 authors, Paul S MacLean.
JCI Insight, 2018 Jul 27; 3(14). PMID: 30046001    Free PMC article.
Fatty acid oxidation is associated with proliferation and prognosis in breast and other cancers.
Aziz Aiderus, Michael A Black, Anita K Dunbier.
BMC Cancer, 2018 Aug 11; 18(1). PMID: 30092766    Free PMC article.
Co-expressed genes enhance precision of receptor status identification in breast cancer patients.
Michael Kenn, Dan Cacsire Castillo-Tong, +3 authors, Wolfgang Schreiner.
Breast Cancer Res Treat, 2018 Aug 18; 172(2). PMID: 30117066    Free PMC article.
Effects of isoflavones on breast tissue and the thyroid hormone system in humans: a comprehensive safety evaluation.
S Hüser, S Guth, +14 authors, S E Kulling.
Arch Toxicol, 2018 Aug 23; 92(9). PMID: 30132047    Free PMC article.
Review.
Feasibility of developing reliable gene expression modules from FFPE derived RNA profiled on Affymetrix arrays.
Vinu Jose, Debora Fumagalli, +4 authors, Christos Sotiriou.
PLoS One, 2018 Sep 01; 13(8). PMID: 30169535    Free PMC article.
The sbv IMPROVER Systems Toxicology Computational Challenge: Identification of Human and Species-Independent Blood Response Markers as Predictors of Smoking Exposure and Cessation Status.
Vincenzo Belcastro, Carine Poussin, +21 authors, Sandeep Kumar Dhanda.
Comput Toxicol, 2018 Sep 18; 5. PMID: 30221212    Free PMC article.
Decentralized Learning Framework of Meta-Survival Analysis for Developing Robust Prognostic Signatures.
Yi Cui, Bailiang Li, Ruijiang Li.
JCO Clin Cancer Inform, 2017 Nov 01; 1. PMID: 30657395    Free PMC article.
DECO: decompose heterogeneous population cohorts for patient stratification and discovery of sample biomarkers using omic data profiling.
F J Campos-Laborie, A Risueño, +7 authors, J De Las Rivas.
Bioinformatics, 2019 Mar 03; 35(19). PMID: 30824909    Free PMC article.
Metadata Analysis Approaches for Understanding and Improving the Functional Involvement of Rumen Microbial Consortium in Digestion and Metabolism of Plant Biomass.
Ayyappa Kumar Sista Kameshwar, Luiz Pereira Ramos, Wensheng Qin.
J Genomics, 2019 Apr 20; 7. PMID: 31001361    Free PMC article.
Review.
Identification of differentially expressed gene sets using the Generalized Berk-Jones statistic.
Sheila M Gaynor, Ryan Sun, Xihong Lin, John Quackenbush.
Bioinformatics, 2019 May 08; 35(22). PMID: 31062858    Free PMC article.
A Toolbox for Functional Analysis and the Systematic Identification of Diagnostic and Prognostic Gene Expression Signatures Combining Meta-Analysis and Machine Learning.
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