Published in Am J Pathol on November 01, 2004
Trial of Pemetrexed and Bevacizumab for Recurrent Ovarian Primary Peritoneal Carcinoma | NCT00868192
Gene expression in fixed tissues and outcome in hepatocellular carcinoma. N Engl J Med (2008) 9.20
Estrogen-dependent signaling in a molecularly distinct subclass of aggressive prostate cancer. J Natl Cancer Inst (2008) 3.55
A re-annotation pipeline for Illumina BeadArrays: improving the interpretation of gene expression data. Nucleic Acids Res (2009) 3.50
Molecular sampling of prostate cancer: a dilemma for predicting disease progression. BMC Med Genomics (2010) 2.40
Whole-genome gene expression profiling of formalin-fixed, paraffin-embedded tissue samples. PLoS One (2009) 2.21
RNA expression analysis from formalin fixed paraffin embedded tissues. Histochem Cell Biol (2008) 2.13
A tissue biomarker panel predicting systemic progression after PSA recurrence post-definitive prostate cancer therapy. PLoS One (2008) 2.09
Successful application of microarray technology to microdissected formalin-fixed, paraffin-embedded tissue. J Mol Diagn (2007) 2.04
Acquisition of biologically relevant gene expression data by Affymetrix microarray analysis of archival formalin-fixed paraffin-embedded tumours. Br J Cancer (2008) 1.74
Optimization of RNA extraction from FFPE tissues for expression profiling in the DASL assay. Biotechniques (2008) 1.72
Basic concepts of microarrays and potential applications in clinical microbiology. Clin Microbiol Rev (2009) 1.70
Gene expression profiles from formalin fixed paraffin embedded breast cancer tissue are largely comparable to fresh frozen matched tissue. PLoS One (2011) 1.56
Identification of novel reference genes using multiplatform expression data and their validation for quantitative gene expression analysis. PLoS One (2009) 1.55
Highly sensitive and specific microRNA expression profiling using BeadArray technology. Nucleic Acids Res (2008) 1.54
HER3 and downstream pathways are involved in colonization of brain metastases from breast cancer. Breast Cancer Res (2010) 1.48
Biomarker discovery for colon cancer using a 761 gene RT-PCR assay. BMC Genomics (2007) 1.46
Gene expression profiling of paraffin-embedded primary melanoma using the DASL assay identifies increased osteopontin expression as predictive of reduced relapse-free survival. Clin Cancer Res (2009) 1.40
mRNA expression signature of Gleason grade predicts lethal prostate cancer. J Clin Oncol (2011) 1.40
Profiling alternatively spliced mRNA isoforms for prostate cancer classification. BMC Bioinformatics (2006) 1.39
Implementing prognostic and predictive biomarkers in CRC clinical trials. Nat Rev Clin Oncol (2011) 1.31
Protein-coding and microRNA biomarkers of recurrence of prostate cancer following radical prostatectomy. Am J Pathol (2011) 1.24
Evaluation of the branched-chain DNA assay for measurement of RNA in formalin-fixed tissues. J Mol Diagn (2008) 1.17
Nanostring-based multigene assay to predict recurrence for gastric cancer patients after surgery. PLoS One (2014) 1.17
Transcriptional profiling of degraded RNA in cryopreserved and fixed tissue samples obtained at autopsy. BMC Clin Pathol (2006) 1.17
Expression profiling with RNA from formalin-fixed, paraffin-embedded material. BMC Med Genomics (2008) 1.16
Androgen modulation of coregulator expression in prostate cancer cells. Mol Endocrinol (2009) 1.14
Analyses and interpretation of whole-genome gene expression from formalin-fixed paraffin-embedded tissue: an illustration with breast cancer tissues. BMC Genomics (2010) 1.13
Salicylic acid-dependent expression of host genes in compatible Arabidopsis-virus interactions. Plant Physiol (2005) 1.13
Patterns of expression of DNA repair genes and relapse from melanoma. Clin Cancer Res (2010) 1.09
An optimized workflow for improved gene expression profiling for formalin-fixed, paraffin-embedded tumor samples. J Clin Bioinforma (2013) 1.05
Differential Expression of Immune-Regulatory Genes Associated with PD-L1 Display in Melanoma: Implications for PD-1 Pathway Blockade. Clin Cancer Res (2015) 1.04
Transcriptome profiling of archived sectioned formalin-fixed paraffin-embedded (AS-FFPE) tissue for disease classification. PLoS One (2014) 1.01
Gene expression array testing of FFPE archival breast tumor samples: an optimized protocol for WG-DASL sample preparation. Breast Cancer Res Treat (2010) 0.95
Development and validation of a 32-gene prognostic index for prostate cancer progression. Proc Natl Acad Sci U S A (2013) 0.95
Risk Prediction for Prostate Cancer Recurrence Through Regularized Estimation with Simultaneous Adjustment for Nonlinear Clinical Effects. Ann Appl Stat (2011) 0.94
Fractalkine is expressed in early and advanced atherosclerotic lesions and supports monocyte recruitment via CX3CR1. PLoS One (2012) 0.93
Potential prognostic biomarkers for bone metastasis from hepatocellular carcinoma. Oncologist (2011) 0.93
Clinical relevance of DNA microarray analyses using archival formalin-fixed paraffin-embedded breast cancer specimens. BMC Cancer (2011) 0.92
Predicting early brain metastases based on clinicopathological factors and gene expression analysis in advanced HER2-positive breast cancer patients. J Neurooncol (2015) 0.90
Imputing gene expression from selectively reduced probe sets. Nat Methods (2012) 0.89
Molecular restoration of archived transcriptional profiles by complementary-template reverse-transcription (CT-RT). Nucleic Acids Res (2007) 0.86
Molecular characterisation of formalin-fixed paraffin-embedded (FFPE) breast tumour specimens using a custom 512-gene breast cancer bead array-based platform. Br J Cancer (2011) 0.85
Quality assessment metrics for whole genome gene expression profiling of paraffin embedded samples. BMC Res Notes (2013) 0.85
Identification and validation of gene expression models that predict clinical outcome in patients with early-stage laryngeal cancer. Ann Oncol (2012) 0.85
Expression profiling of formalin-fixed paraffin-embedded primary breast tumors using cancer-specific and whole genome gene panels on the DASL® platform. BMC Med Genomics (2010) 0.84
A systems approach to clinical oncology: focus on breast cancer. Proteome Sci (2006) 0.84
Upregulated FGFR1 expression is associated with the transition of hormone-naive to castrate-resistant prostate cancer. Br J Cancer (2011) 0.83
Genomic markers for decision making: what is preventing us from using markers? Nat Rev Clin Oncol (2009) 0.82
Analysis of multiple sarcoma expression datasets: implications for classification, oncogenic pathway activation and chemotherapy resistance. PLoS One (2010) 0.82
A methodology for utilization of predictive genomic signatures in FFPE samples. BMC Med Genomics (2011) 0.80
Transcriptional profiling of formalin fixed paraffin embedded tissue: pitfalls and recommendations for identifying biologically relevant changes. PLoS One (2012) 0.79
Accurate data processing improves the reliability of Affymetrix gene expression profiles from FFPE samples. PLoS One (2014) 0.79
A multiplex endpoint RT-PCR assay for quality assessment of RNA extracted from formalin-fixed paraffin-embedded tissues. BMC Biotechnol (2010) 0.78
Expression profiling of formalin-fixed paraffin embedded primary human uveal melanomas using DASL matrices. J Cancer Res Clin Oncol (2009) 0.78
qPCR in gastrointestinal stromal tumors: Evaluation of reference genes and expression analysis of KIT and the alternative receptor tyrosine kinases FLT3, CSF1-R, PDGFRB, MET and AXL. BMC Mol Biol (2010) 0.78
Genome-wide expression assay comparison across frozen and fixed postmortem brain tissue samples. BMC Genomics (2011) 0.77
Gene expression profiling of human hepatoblastoma using archived formalin-fixed and paraffin-embedded tissues. Virchows Arch (2011) 0.77
Prognostic implication of morphology, cyclinE2 and proliferation in EBV-associated T/NK lymphoproliferative disease in non-immunocompromised hosts. Orphanet J Rare Dis (2014) 0.76
Integration of genetic signature and TNM staging system for predicting the relapse of locally advanced colorectal cancer. Int J Colorectal Dis (2010) 0.76
Use of formalin-fixed paraffin-embedded samples for gene expression studies in breast cancer patients. PLoS One (2015) 0.75
Reliable gene expression profiling of formalin-fixed paraffin-embedded breast cancer tissue (FFPE) using cDNA-mediated annealing, extension, selection, and ligation whole-genome (DASL WG) assay. BMC Med Genomics (2016) 0.75
Protruding disordered loop of gC1qR is specifically exposed and related to antiapoptotic property in germ cell lineage. Histochem Cell Biol (2006) 0.75
Identification and validation of differentially expressed transcripts by RNA-sequencing of formalin-fixed, paraffin-embedded (FFPE) lung tissue from patients with Idiopathic Pulmonary Fibrosis. BMC Pulm Med (2017) 0.75
Integrative analysis of copy number and gene expression in breast cancer using formalin-fixed paraffin-embedded core biopsy tissue: a feasibility study. BMC Genomics (2017) 0.75
Molecular portraits of human breast tumours. Nature (2000) 94.14
Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science (1999) 83.27
Expression monitoring by hybridization to high-density oligonucleotide arrays. Nat Biotechnol (1996) 72.84
Gene expression profiling predicts clinical outcome of breast cancer. Nature (2002) 71.36
Predicting the clinical status of human breast cancer by using gene expression profiles. Proc Natl Acad Sci U S A (2001) 13.30
Delineation of prognostic biomarkers in prostate cancer. Nature (2001) 12.25
Highly parallel SNP genotyping. Cold Spring Harb Symp Quant Biol (2003) 9.10
A new non-linear normalization method for reducing variability in DNA microarray experiments. Genome Biol (2002) 7.12
Analysis of gene expression identifies candidate markers and pharmacological targets in prostate cancer. Cancer Res (2001) 6.73
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
A versatile assay for high-throughput gene expression profiling on universal array matrices. Genome Res (2004) 4.19
Quantitative gene expression analysis in microdissected archival formalin-fixed and paraffin-embedded tumor tissue. Am J Pathol (2001) 4.18
Quantitative mRNA expression analysis from formalin-fixed, paraffin-embedded tissues using 5' nuclease quantitative reverse transcription-polymerase chain reaction. J Mol Diagn (2000) 3.59
Decoding randomly ordered DNA arrays. Genome Res (2004) 3.49
Unlocking the archive--gene expression in paraffin-embedded tissue. J Pathol (2001) 2.76
Antisense RNA Amplification: A Linear Amplification Method for Analyzing the mRNA Population from Single Living Cells Methods (1996) 2.60
Towards quantitative mRNA analysis in paraffin-embedded tissues using real-time reverse transcriptase-polymerase chain reaction: a methodological study on lymph nodes from melanoma patients. J Mol Diagn (2003) 2.41
An evaluation of tyramide signal amplification and archived fixed and frozen tissue in microarray gene expression analysis. Nucleic Acids Res (2002) 2.06
Prognostic value of ERBB family mRNA expression in breast carcinomas. Int J Cancer (2003) 1.95
Automatic registration of microarray images. II. Hexagonal grid. Bioinformatics (2003) 1.70
Detection of gene amplification in archival breast cancer specimens by laser-assisted microdissection and quantitative real-time polymerase chain reaction. Am J Pathol (2000) 1.55
Macrophage inhibitory cytokine-1 induces the invasiveness of gastric cancer cells by up-regulating the urokinase-type plasminogen activator system. Cancer Res (2003) 1.45
Down-regulation of (IIIb) and (IIIc) isoforms of fibroblast growth factor receptor 2 (FGFR2) is associated with malignant progression in human prostate. Prostate (2002) 1.10
Identification of Down's syndrome critical locus gene SIM2-s as a drug therapy target for solid tumors. Proc Natl Acad Sci U S A (2003) 1.09
Quantitative molecular analysis of laser-microdissected paraffin-embedded human tissues. Pathobiology (2000) 1.02
Down's syndrome-associated single minded gene as a novel tumor marker. Anticancer Res (2003) 1.00
Detection of occult melanoma cells in paraffin-embedded histologically negative sentinel lymph nodes using a reverse transcriptase polymerase chain reaction assay. J Clin Oncol (2001) 0.92
IGF-I in human breast cancer: low differentiation stage is associated with decreased IGF-I content. Eur J Endocrinol (2002) 0.91
Retroviral infection of the FGF2 gene into MCF-7 cells induces branching morphogenesis, retards cell growth and suppresses tumorigenicity in nude mice. Eur J Cancer (2001) 0.84
A second generation human haplotype map of over 3.1 million SNPs. Nature (2007) 85.39
The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements. Nat Biotechnol (2006) 30.90
Gene-expression profiles to predict distant metastasis of lymph-node-negative primary breast cancer. Lancet (2005) 29.45
Grading quality of evidence and strength of recommendations. BMJ (2004) 26.08
Mapping the genetic architecture of gene expression in human liver. PLoS Biol (2008) 19.44
Genome-wide detection and characterization of positive selection in human populations. Nature (2007) 17.27
Major causes of death among men and women in China. N Engl J Med (2005) 11.80
High density DNA methylation array with single CpG site resolution. Genomics (2011) 10.35
Strong time dependence of the 76-gene prognostic signature for node-negative breast cancer patients in the TRANSBIG multicenter independent validation series. Clin Cancer Res (2007) 8.41
High-throughput DNA methylation profiling using universal bead arrays. Genome Res (2006) 8.05
FGF23 induces left ventricular hypertrophy. J Clin Invest (2011) 7.22
Developmental plasticity and human health. Nature (2004) 7.13
Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq. Genome Res (2011) 6.90
Frequent mutations of chromatin remodeling genes in transitional cell carcinoma of the bladder. Nat Genet (2011) 5.73
Tyrosine phosphorylation inhibits PKM2 to promote the Warburg effect and tumor growth. Sci Signal (2009) 5.57
A family of diverse Cul4-Ddb1-interacting proteins includes Cdt2, which is required for S phase destruction of the replication factor Cdt1. Mol Cell (2006) 5.51
Quantitative phenotyping via deep barcode sequencing. Genome Res (2009) 5.13
Gene expression profiles and molecular markers to predict recurrence of Dukes' B colon cancer. J Clin Oncol (2004) 5.12
GRADE guidelines: 4. Rating the quality of evidence--study limitations (risk of bias). J Clin Epidemiol (2011) 5.10
Impact of creatinine calibration on performance of GFR estimating equations in a pooled individual patient database. Am J Kidney Dis (2007) 5.06
Prevalence of the metabolic syndrome and overweight among adults in China. Lancet (2005) 5.05
Mortality attributable to smoking in China. N Engl J Med (2009) 4.75
Fibroblast growth factor 23 is elevated before parathyroid hormone and phosphate in chronic kidney disease. Kidney Int (2011) 4.74
Young age at diagnosis correlates with worse prognosis and defines a subset of breast cancers with shared patterns of gene expression. J Clin Oncol (2008) 4.45
Community cyberinfrastructure for Advanced Microbial Ecology Research and Analysis: the CAMERA resource. Nucleic Acids Res (2010) 4.39
Subtypes of breast cancer show preferential site of relapse. Cancer Res (2008) 4.38
A novel, high-performance random array platform for quantitative gene expression profiling. Genome Res (2004) 4.32
A versatile assay for high-throughput gene expression profiling on universal array matrices. Genome Res (2004) 4.19
Prevalence, awareness, treatment, and control of hypertension in china. Hypertension (2002) 4.18
Gene expression signatures for predicting prognosis of squamous cell and adenocarcinomas of the lung. Cancer Res (2006) 4.11
The genomic sequence of the accidental pathogen Legionella pneumophila. Science (2004) 4.08
Profiling alternative splicing on fiber-optic arrays. Nat Biotechnol (2002) 3.94
Differential allelic expression in the human genome: a robust approach to identify genetic and epigenetic cis-acting mechanisms regulating gene expression. PLoS Genet (2008) 3.92
Lung metastasis genes couple breast tumor size and metastatic spread. Proc Natl Acad Sci U S A (2007) 3.92
Whole-genome and whole-exome sequencing of bladder cancer identifies frequent alterations in genes involved in sister chromatid cohesion and segregation. Nat Genet (2013) 3.87
The contribution of health literacy to disparities in self-rated health status and preventive health behaviors in older adults. Ann Fam Med (2009) 3.84
High-throughput SNP genotyping on universal bead arrays. Mutat Res (2005) 3.78
Frequent mutations of genes encoding ubiquitin-mediated proteolysis pathway components in clear cell renal cell carcinoma. Nat Genet (2011) 3.66
Assuring the quality of next-generation sequencing in clinical laboratory practice. Nat Biotechnol (2012) 3.62
GRADE guidelines: 2. Framing the question and deciding on important outcomes. J Clin Epidemiol (2010) 3.60
DNA methylation signatures within the human brain. Am J Hum Genet (2007) 3.50
Decoding randomly ordered DNA arrays. Genome Res (2004) 3.49
GRADE guidelines: 5. Rating the quality of evidence--publication bias. J Clin Epidemiol (2011) 3.44
Body weight and mortality among men and women in China. JAMA (2006) 3.41
Quantification of oxygen-induced retinopathy in the mouse: a model of vessel loss, vessel regrowth and pathological angiogenesis. Nat Protoc (2009) 3.31
GRADE guidelines: 9. Rating up the quality of evidence. J Clin Epidemiol (2011) 3.30
Novel genes associated with malignant melanoma but not benign melanocytic lesions. Clin Cancer Res (2005) 3.30
Identification of a ferrireductase required for efficient transferrin-dependent iron uptake in erythroid cells. Nat Genet (2005) 3.28
Effective and selective targeting of leukemia cells using a TORC1/2 kinase inhibitor. Nat Med (2010) 3.26
Genetic test evaluation: information needs of clinicians, policy makers, and the public. Am J Epidemiol (2002) 3.23
Genes associated with breast cancer metastatic to bone. J Clin Oncol (2006) 3.21
Using RNA sample titrations to assess microarray platform performance and normalization techniques. Nat Biotechnol (2006) 3.13
Epigenomic analysis detects widespread gene-body DNA hypomethylation in chronic lymphocytic leukemia. Nat Genet (2012) 3.08
Functional analysis of human microtubule-based motor proteins, the kinesins and dyneins, in mitosis/cytokinesis using RNA interference. Mol Biol Cell (2005) 3.04
A survey of the genetics of stomach, liver, and adipose gene expression from a morbidly obese cohort. Genome Res (2011) 3.00
The prevalence of nontraditional risk factors for coronary heart disease in patients with chronic kidney disease. Ann Intern Med (2004) 2.94
Human embryonic stem cells have a unique epigenetic signature. Genome Res (2006) 2.89
Illumina universal bead arrays. Methods Enzymol (2006) 2.88
Effect of soybean protein on blood pressure: a randomized, controlled trial. Ann Intern Med (2005) 2.79
Molecular profiling of carcinoma of unknown primary and correlation with clinical evaluation. J Clin Oncol (2008) 2.78
Store-dependent and -independent modes regulating Ca2+ release-activated Ca2+ channel activity of human Orai1 and Orai3. J Biol Chem (2008) 2.75
A highly informative SNP linkage panel for human genetic studies. Nat Methods (2004) 2.74
microRNA-29a induces aberrant self-renewal capacity in hematopoietic progenitors, biased myeloid development, and acute myeloid leukemia. J Exp Med (2010) 2.68
Combining clinical, pathology, and gene expression data to predict recurrence of hepatocellular carcinoma. Gastroenterology (2011) 2.66
AHRQ series paper 5: grading the strength of a body of evidence when comparing medical interventions--agency for healthcare research and quality and the effective health-care program. J Clin Epidemiol (2010) 2.63
Premature deaths attributable to blood pressure in China: a prospective cohort study. Lancet (2009) 2.62
Tyrosine phosphorylation of mitochondrial pyruvate dehydrogenase kinase 1 is important for cancer metabolism. Mol Cell (2011) 2.61
Resiniferatoxin for treatment of lifelong premature ejaculation: a preliminary study. Int J Urol (2014) 2.61
The mouse retina as an angiogenesis model. Invest Ophthalmol Vis Sci (2010) 2.61
Genome-wide genetic changes during modern breeding of maize. Nat Genet (2012) 2.60
MicroRNA function is globally suppressed in mouse oocytes and early embryos. Curr Biol (2010) 2.57
FGFR3 activates RSK2 to mediate hematopoietic transformation through tyrosine phosphorylation of RSK2 and activation of the MEK/ERK pathway. Cancer Cell (2007) 2.56
Comprehensive microRNA profiling reveals a unique human embryonic stem cell signature dominated by a single seed sequence. Stem Cells (2008) 2.52
Actin and Arf1-dependent recruitment of a cortactin-dynamin complex to the Golgi regulates post-Golgi transport. Nat Cell Biol (2005) 2.50
Visfatin induces human endothelial VEGF and MMP-2/9 production via MAPK and PI3K/Akt signalling pathways: novel insights into visfatin-induced angiogenesis. Cardiovasc Res (2007) 2.49
Multicenter validation of a gene expression-based prognostic signature in lymph node-negative primary breast cancer. J Clin Oncol (2006) 2.48
H3K9 methylation is a barrier during somatic cell reprogramming into iPSCs. Nat Genet (2012) 2.47
Pax6 is a human neuroectoderm cell fate determinant. Cell Stem Cell (2010) 2.46
Sequencing and automated whole-genome optical mapping of the genome of a domestic goat (Capra hircus). Nat Biotechnol (2012) 2.45