Published in Nature on January 31, 2002
Comprehensive molecular portraits of human breast tumours. Nature (2012) 47.39
Repeated observation of breast tumor subtypes in independent gene expression data sets. Proc Natl Acad Sci U S A (2003) 34.68
ALDH1 is a marker of normal and malignant human mammary stem cells and a predictor of poor clinical outcome. Cell Stem Cell (2007) 22.89
Supervised risk predictor of breast cancer based on intrinsic subtypes. J Clin Oncol (2009) 22.22
Genes that mediate breast cancer metastasis to lung. Nature (2005) 19.85
ONCOMINE: a cancer microarray database and integrated data-mining platform. Neoplasia (2004) 17.08
EZH2 is a marker of aggressive breast cancer and promotes neoplastic transformation of breast epithelial cells. Proc Natl Acad Sci U S A (2003) 13.68
An expression signature for p53 status in human breast cancer predicts mutation status, transcriptional effects, and patient survival. Proc Natl Acad Sci U S A (2005) 13.54
Breast cancer classification and prognosis based on gene expression profiles from a population-based study. Proc Natl Acad Sci U S A (2003) 13.00
Gene selection and classification of microarray data using random forest. BMC Bioinformatics (2006) 12.45
The molecular portraits of breast tumors are conserved across microarray platforms. BMC Genomics (2006) 12.45
Network-based classification of breast cancer metastasis. Mol Syst Biol (2007) 12.18
GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists. BMC Bioinformatics (2009) 12.01
An integrative genomics approach to infer causal associations between gene expression and disease. Nat Genet (2005) 11.40
Phenotypic and molecular characterization of the claudin-low intrinsic subtype of breast cancer. Breast Cancer Res (2010) 10.90
Robustness, scalability, and integration of a wound-response gene expression signature in predicting breast cancer survival. Proc Natl Acad Sci U S A (2005) 10.85
Identification of conserved gene expression features between murine mammary carcinoma models and human breast tumors. Genome Biol (2007) 10.49
Tumor metastasis: molecular insights and evolving paradigms. Cell (2011) 10.34
Large-scale meta-analysis of cancer microarray data identifies common transcriptional profiles of neoplastic transformation and progression. Proc Natl Acad Sci U S A (2004) 9.42
Gene expression signature of fibroblast serum response predicts human cancer progression: similarities between tumors and wounds. PLoS Biol (2004) 9.38
Coexpression analysis of human genes across many microarray data sets. Genome Res (2004) 9.38
Onto-Tools, the toolkit of the modern biologist: Onto-Express, Onto-Compare, Onto-Design and Onto-Translate. Nucleic Acids Res (2003) 9.30
Initial impact of the sequencing of the human genome. Nature (2011) 9.18
Genetic inheritance of gene expression in human cell lines. Am J Hum Genet (2004) 8.97
Gene expression profiling spares early breast cancer patients from adjuvant therapy: derived and validated in two population-based cohorts. Breast Cancer Res (2005) 8.73
REVIGO summarizes and visualizes long lists of gene ontology terms. PLoS One (2011) 8.65
Molecular basis of metastasis. N Engl J Med (2008) 8.19
Representational oligonucleotide microarray analysis: a high-resolution method to detect genome copy number variation. Genome Res (2003) 7.86
Semi-supervised methods to predict patient survival from gene expression data. PLoS Biol (2004) 7.68
Human breast cancer cell lines contain stem-like cells that self-renew, give rise to phenotypically diverse progeny and survive chemotherapy. Breast Cancer Res (2008) 7.65
The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models. Nat Biotechnol (2010) 7.08
A systems biology approach for pathway level analysis. Genome Res (2007) 6.95
Reliability and reproducibility issues in DNA microarray measurements. Trends Genet (2005) 6.79
Meta-analysis of gene expression profiles in breast cancer: toward a unified understanding of breast cancer subtyping and prognosis signatures. Breast Cancer Res (2008) 6.63
MicroRNA expression profiling of human breast cancer identifies new markers of tumor subtype. Genome Biol (2007) 6.41
CD44+/CD24- breast cancer cells exhibit enhanced invasive properties: an early step necessary for metastasis. Breast Cancer Res (2006) 6.35
Gene expression profiles of human breast cancer progression. Proc Natl Acad Sci U S A (2003) 6.35
Analysis of oncogenic signaling networks in glioblastoma identifies ASPM as a molecular target. Proc Natl Acad Sci U S A (2006) 6.33
Thousands of samples are needed to generate a robust gene list for predicting outcome in cancer. Proc Natl Acad Sci U S A (2006) 6.26
Heterogeneity of breast cancer associations with five susceptibility loci by clinical and pathological characteristics. PLoS Genet (2008) 6.22
Distinct organ-specific metastatic potential of individual breast cancer cells and primary tumors. J Clin Invest (2005) 6.10
Gene expression programs in response to hypoxia: cell type specificity and prognostic significance in human cancers. PLoS Med (2006) 6.04
A Myc network accounts for similarities between embryonic stem and cancer cell transcription programs. Cell (2010) 6.00
Microarray analysis identifies a death-from-cancer signature predicting therapy failure in patients with multiple types of cancer. J Clin Invest (2005) 5.90
Mad2 overexpression promotes aneuploidy and tumorigenesis in mice. Cancer Cell (2006) 5.88
Whole-genome cartography of estrogen receptor alpha binding sites. PLoS Genet (2007) 5.85
Poor prognosis in carcinoma is associated with a gene expression signature of aberrant PTEN tumor suppressor pathway activity. Proc Natl Acad Sci U S A (2007) 5.44
Measurement of gene expression in archival paraffin-embedded tissues: development and performance of a 92-gene reverse transcriptase-polymerase chain reaction assay. Am J Pathol (2004) 5.29
Mesenchyme Forkhead 1 (FOXC2) plays a key role in metastasis and is associated with aggressive basal-like breast cancers. Proc Natl Acad Sci U S A (2007) 5.24
Heat shock proteins in cancer: diagnostic, prognostic, predictive, and treatment implications. Cell Stress Chaperones (2005) 5.22
GATA-3 maintains the differentiation of the luminal cell fate in the mammary gland. Cell (2006) 4.98
AACR centennial series: the biology of cancer metastasis: historical perspective. Cancer Res (2010) 4.89
From latent disseminated cells to overt metastasis: genetic analysis of systemic breast cancer progression. Proc Natl Acad Sci U S A (2003) 4.79
High-resolution aCGH and expression profiling identifies a novel genomic subtype of ER negative breast cancer. Genome Biol (2007) 4.70
Systematic analysis and nomenclature of mammalian F-box proteins. Genes Dev (2004) 4.68
Breast cancer subtypes and response to docetaxel in node-positive breast cancer: use of an immunohistochemical definition in the BCIRG 001 trial. J Clin Oncol (2009) 4.66
RNAscope: a novel in situ RNA analysis platform for formalin-fixed, paraffin-embedded tissues. J Mol Diagn (2012) 4.63
Molecular profiling of breast cancer cell lines defines relevant tumor models and provides a resource for cancer gene discovery. PLoS One (2009) 4.62
A comparison of PAM50 intrinsic subtyping with immunohistochemistry and clinical prognostic factors in tamoxifen-treated estrogen receptor-positive breast cancer. Clin Cancer Res (2010) 4.61
Gene expression profiling predicts clinical outcome of prostate cancer. J Clin Invest (2004) 4.59
Converting a breast cancer microarray signature into a high-throughput diagnostic test. BMC Genomics (2006) 4.57
MTDH activation by 8q22 genomic gain promotes chemoresistance and metastasis of poor-prognosis breast cancer. Cancer Cell (2009) 4.47
Gene expression profiles of primary breast tumors maintained in distant metastases. Proc Natl Acad Sci U S A (2003) 4.47
Ki-67 as prognostic marker in early breast cancer: a meta-analysis of published studies involving 12,155 patients. Br J Cancer (2007) 4.44
Sequence-matched probes produce increased cross-platform consistency and more reproducible biological results in microarray-based gene expression measurements. Nucleic Acids Res (2004) 4.43
Prognostic utility of the 21-gene assay in hormone receptor-positive operable breast cancer compared with classical clinicopathologic features. J Clin Oncol (2008) 4.42
Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res (2007) 4.41
On the C-statistics for evaluating overall adequacy of risk prediction procedures with censored survival data. Stat Med (2011) 4.34
An immune response gene expression module identifies a good prognosis subtype in estrogen receptor negative breast cancer. Genome Biol (2007) 4.33
A novel, high-performance random array platform for quantitative gene expression profiling. Genome Res (2004) 4.32
A population-based study of tumor gene expression and risk of breast cancer death among lymph node-negative patients. Breast Cancer Res (2006) 4.28
Novel patterns of genome rearrangement and their association with survival in breast cancer. Genome Res (2006) 4.25
A versatile assay for high-throughput gene expression profiling on universal array matrices. Genome Res (2004) 4.19
From the Cover: Location analysis of estrogen receptor alpha target promoters reveals that FOXA1 defines a domain of the estrogen response. Proc Natl Acad Sci U S A (2005) 4.16
Genetic prognostic and predictive markers in colorectal cancer. Nat Rev Cancer (2009) 3.99
Triple-negative breast cancer: disease entity or title of convenience? Nat Rev Clin Oncol (2010) 3.98
Genetic regulators of large-scale transcriptional signatures in cancer. Nat Genet (2006) 3.96
Metastasis: recent discoveries and novel treatment strategies. Lancet (2007) 3.93
Lung metastasis genes couple breast tumor size and metastatic spread. Proc Natl Acad Sci U S A (2007) 3.92
Gastric adenocarcinoma: review and considerations for future directions. Ann Surg (2005) 3.83
Association between the 21-gene recurrence score assay and risk of locoregional recurrence in node-negative, estrogen receptor-positive breast cancer: results from NSABP B-14 and NSABP B-20. J Clin Oncol (2010) 3.79
TGF-beta and the Smad signaling pathway support transcriptomic reprogramming during epithelial-mesenchymal cell transition. Mol Biol Cell (2005) 3.75
Specificity of short interfering RNA determined through gene expression signatures. Proc Natl Acad Sci U S A (2003) 3.74
Insulin-like growth factor-I activates gene transcription programs strongly associated with poor breast cancer prognosis. J Clin Oncol (2008) 3.74
The cofilin pathway in breast cancer invasion and metastasis. Nat Rev Cancer (2007) 3.71
Heterogeneity of breast cancer metastases: comparison of therapeutic target expression and promoter methylation between primary tumors and their multifocal metastases. Clin Cancer Res (2008) 3.67
Trans-eQTLs reveal that independent genetic variants associated with a complex phenotype converge on intermediate genes, with a major role for the HLA. PLoS Genet (2011) 3.65
Revisiting global gene expression analysis. Cell (2012) 3.63
Gene Expression Atlas update--a value-added database of microarray and sequencing-based functional genomics experiments. Nucleic Acids Res (2011) 3.61
Transcriptional pathway signatures predict MEK addiction and response to selumetinib (AZD6244). Cancer Res (2010) 3.54
Decoding randomly ordered DNA arrays. Genome Res (2004) 3.49
Inferring pathway activity toward precise disease classification. PLoS Comput Biol (2008) 3.48
GATA-3 links tumor differentiation and dissemination in a luminal breast cancer model. Cancer Cell (2008) 3.44
methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles. Genome Biol (2012) 3.44
The properties of high-dimensional data spaces: implications for exploring gene and protein expression data. Nat Rev Cancer (2008) 3.43
ChEA: transcription factor regulation inferred from integrating genome-wide ChIP-X experiments. Bioinformatics (2010) 3.42
Tumor cells disseminate early, but immunosurveillance limits metastatic outgrowth, in a mouse model of melanoma. J Clin Invest (2010) 3.41
Gene expression analyses reveal molecular relationships among 20 regions of the human CNS. Neurogenetics (2006) 3.40
The UCSC Cancer Genomics Browser: update 2011. Nucleic Acids Res (2010) 3.37
A gene expression signature predicts survival of patients with stage I non-small cell lung cancer. PLoS Med (2006) 3.37
A gene-expression signature as a predictor of survival in breast cancer. N Engl J Med (2002) 58.15
Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs. Nature (2005) 48.95
A system for stable expression of short interfering RNAs in mammalian cells. Science (2002) 35.21
Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis. Nature (2010) 23.55
Genetics of gene expression surveyed in maize, mouse and man. Nature (2003) 22.17
A microRNA component of the p53 tumour suppressor network. Nature (2007) 19.25
Expression profiling reveals off-target gene regulation by RNAi. Nat Biotechnol (2003) 16.63
A functional genetic approach identifies the PI3K pathway as a major determinant of trastuzumab resistance in breast cancer. Cancer Cell (2007) 11.21
Robustness, scalability, and integration of a wound-response gene expression signature in predicting breast cancer survival. Proc Natl Acad Sci U S A (2005) 10.85
Systematic protein location mapping reveals five principal chromatin types in Drosophila cells. Cell (2010) 9.50
Unresponsiveness of colon cancer to BRAF(V600E) inhibition through feedback activation of EGFR. Nature (2012) 9.39
A genomic and functional inventory of deubiquitinating enzymes. Cell (2005) 9.36
A large-scale RNAi screen in human cells identifies new components of the p53 pathway. Nature (2004) 8.67
Genes that mediate breast cancer metastasis to the brain. Nature (2009) 8.23
An integrative genomic and proteomic analysis of PIK3CA, PTEN, and AKT mutations in breast cancer. Cancer Res (2008) 8.12
Stable suppression of tumorigenicity by virus-mediated RNA interference. Cancer Cell (2002) 7.88
Widespread siRNA "off-target" transcript silencing mediated by seed region sequence complementarity. RNA (2006) 7.06
FoxM1 is required for execution of the mitotic programme and chromosome stability. Nat Cell Biol (2005) 7.02
Molecular maps of the reorganization of genome-nuclear lamina interactions during differentiation. Mol Cell (2010) 6.71
Loss of the cylindromatosis tumour suppressor inhibits apoptosis by activating NF-kappaB. Nature (2003) 6.53
Transcripts targeted by the microRNA-16 family cooperatively regulate cell cycle progression. Mol Cell Biol (2007) 6.43
Academic performance of ethnic minority candidates and discrimination in the MRCGP examinations between 2010 and 2012: analysis of data. BMJ (2013) 6.22
CTLA-4 and PD-1 receptors inhibit T-cell activation by distinct mechanisms. Mol Cell Biol (2005) 6.18
Gene expression programs in response to hypoxia: cell type specificity and prognostic significance in human cancers. PLoS Med (2006) 6.04
Minimizing the risk of reporting false positives in large-scale RNAi screens. Nat Methods (2006) 5.96
Medical assessment of adverse health outcomes in long-term survivors of childhood cancer. JAMA (2007) 5.74
Participation and yield of colonoscopy versus non-cathartic CT colonography in population-based screening for colorectal cancer: a randomised controlled trial. Lancet Oncol (2011) 5.72
Exome sequencing identifies frequent mutation of ARID1A in molecular subtypes of gastric cancer. Nat Genet (2011) 5.68
Tumor exome analysis reveals neoantigen-specific T-cell reactivity in an ipilimumab-responsive melanoma. J Clin Oncol (2013) 5.23
MicroRNA 21 promotes glioma invasion by targeting matrix metalloproteinase regulators. Mol Cell Biol (2008) 5.21
Single-cell exome sequencing and monoclonal evolution of a JAK2-negative myeloproliferative neoplasm. Cell (2012) 5.16
MicroRNAs in the miR-106b family regulate p21/CDKN1A and promote cell cycle progression. Mol Cell Biol (2008) 4.76
Position-specific chemical modification of siRNAs reduces "off-target" transcript silencing. RNA (2006) 4.72
Regulation of monoubiquitinated PCNA by DUB autocleavage. Nat Cell Biol (2006) 4.67
Rosetta error model for gene expression analysis. Bioinformatics (2006) 4.67
Converting a breast cancer microarray signature into a high-throughput diagnostic test. BMC Genomics (2006) 4.57
Plasminogen activator inhibitor-1 is a critical downstream target of p53 in the induction of replicative senescence. Nat Cell Biol (2006) 4.54
Guidelines for Reporting Reliability and Agreement Studies (GRRAS) were proposed. J Clin Epidemiol (2010) 4.50
Gene expression profiles of primary breast tumors maintained in distant metastases. Proc Natl Acad Sci U S A (2003) 4.47
Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res (2007) 4.41
The deubiquitinating enzyme USP1 regulates the Fanconi anemia pathway. Mol Cell (2005) 4.40
The KLF4 tumour suppressor is a transcriptional repressor of p53 that acts as a context-dependent oncogene. Nat Cell Biol (2005) 4.29
Recognizing and avoiding siRNA off-target effects for target identification and therapeutic application. Nat Rev Drug Discov (2010) 4.25
Enabling personalized cancer medicine through analysis of gene-expression patterns. Nature (2008) 4.24
Validity of self-reported height and weight and predictors of bias in adolescents. J Adolesc Health (2005) 4.09
Integrated genomic and proteomic analyses of gene expression in Mammalian cells. Mol Cell Proteomics (2004) 4.09
Genome-wide survey of recurrent HBV integration in hepatocellular carcinoma. Nat Genet (2012) 4.07
Rational development of LEA29Y (belatacept), a high-affinity variant of CTLA4-Ig with potent immunosuppressive properties. Am J Transplant (2005) 4.05
Predictive, personalized, preventive, participatory (P4) cancer medicine. Nat Rev Clin Oncol (2011) 4.02
MED12 controls the response to multiple cancer drugs through regulation of TGF-β receptor signaling. Cell (2012) 4.01
Genetic regulators of large-scale transcriptional signatures in cancer. Nat Genet (2006) 3.96
Effects of atmospheric ozone on microarray data quality. Anal Chem (2003) 3.93
miR-146a is a significant brake on autoimmunity, myeloproliferation, and cancer in mice. J Exp Med (2011) 3.78
Protein phosphatase 2A regulatory subunits and cancer. Biochim Biophys Acta (2008) 3.74
Phosphatidylinositol 3-kinase hyperactivation results in lapatinib resistance that is reversed by the mTOR/phosphatidylinositol 3-kinase inhibitor NVP-BEZ235. Cancer Res (2008) 3.70
Gene expression changes associated with progression and response in chronic myeloid leukemia. Proc Natl Acad Sci U S A (2006) 3.70
Systematic analysis of breast cancer morphology uncovers stromal features associated with survival. Sci Transl Med (2011) 3.68
Synthetic shRNAs as potent RNAi triggers. Nat Biotechnol (2004) 3.67
Somatic loss of BRCA1 and p53 in mice induces mammary tumors with features of human BRCA1-mutated basal-like breast cancer. Proc Natl Acad Sci U S A (2007) 3.58
Microarray standard data set and figures of merit for comparing data processing methods and experiment designs. Bioinformatics (2003) 3.33
Use of 70-gene signature to predict prognosis of patients with node-negative breast cancer: a prospective community-based feasibility study (RASTER). Lancet Oncol (2007) 3.32
Genomic portrait of resectable hepatocellular carcinomas: implications of RB1 and FGF19 aberrations for patient stratification. Hepatology (2014) 3.31
Designing siRNA that distinguish between genes that differ by a single nucleotide. PLoS Genet (2006) 3.23
Human immunodeficiency virus type 1 escapes from RNA interference-mediated inhibition. J Virol (2004) 3.23
Use of intensive case management to reduce time in hospital in people with severe mental illness: systematic review and meta-regression. BMJ (2007) 3.22
High-dose chemotherapy with hematopoietic stem-cell rescue for high-risk breast cancer. N Engl J Med (2003) 3.15
MicroRNA miR-210 modulates cellular response to hypoxia through the MYC antagonist MNT. Cell Cycle (2009) 3.07
MicroRNA sequence and expression analysis in breast tumors by deep sequencing. Cancer Res (2011) 3.02
ZNF423 is critically required for retinoic acid-induced differentiation and is a marker of neuroblastoma outcome. Cancer Cell (2009) 2.93
An shRNA barcode screen provides insight into cancer cell vulnerability to MDM2 inhibitors. Nat Chem Biol (2006) 2.91
A network view of disease and compound screening. Nat Rev Drug Discov (2009) 2.90
Coordinated regulation of cell cycle transcripts by p53-Inducible microRNAs, miR-192 and miR-215. Cancer Res (2008) 2.86