Published in PLoS One on May 21, 2009
Increased methylation variation in epigenetic domains across cancer types. Nat Genet (2011) 8.92
Online survival analysis software to assess the prognostic value of biomarkers using transcriptomic data in non-small-cell lung cancer. PLoS One (2013) 4.31
A comprehensive comparison of RNA-Seq-based transcriptome analysis from reads to differential gene expression and cross-comparison with microarrays: a case study in Saccharomyces cerevisiae. Nucleic Acids Res (2012) 2.53
A molecular mechanism that links Hippo signalling to the inhibition of Wnt/β-catenin signalling. EMBO J (2012) 1.81
Gene expression patterns unveil a new level of molecular heterogeneity in colorectal cancer. J Pathol (2013) 1.71
Large-scale hypomethylated blocks associated with Epstein-Barr virus-induced B-cell immortalization. Genome Res (2013) 1.34
Algorithm-driven artifacts in median Polish summarization of microarray data. BMC Bioinformatics (2010) 1.33
Association of RB/p16-pathway perturbations with DCIS recurrence: dependence on tumor versus tissue microenvironment. Am J Pathol (2011) 1.12
The identification of gene expression profiles associated with progression of human diabetic neuropathy. Brain (2011) 1.12
Gene signature of the metastatic potential of cutaneous melanoma: too much for too little? Clin Exp Metastasis (2010) 1.11
Gene expression anti-profiles as a basis for accurate universal cancer signatures. BMC Bioinformatics (2012) 1.07
Pleiotropic functions of EAPII/TTRAP/TDP2: cancer development, chemoresistance and beyond. Cell Cycle (2011) 0.99
Matrix metalloproteinase-10 promotes Kras-mediated bronchio-alveolar stem cell expansion and lung cancer formation. PLoS One (2011) 0.97
Pathway-based evaluation in early onset colorectal cancer suggests focal adhesion and immunosuppression along with epithelial-mesenchymal transition. PLoS One (2012) 0.90
'Neuroinflammation' differs categorically from inflammation: transcriptomes of Alzheimer's disease, Parkinson's disease, schizophrenia and inflammatory diseases compared. Neurogenetics (2014) 0.88
Inferring drug-disease associations from integration of chemical, genomic and phenotype data using network propagation. BMC Med Genomics (2013) 0.87
A genome-wide approach to link genotype to clinical outcome by utilizing next generation sequencing and gene chip data of 6,697 breast cancer patients. Genome Med (2015) 0.85
Comparative study on gene set and pathway topology-based enrichment methods. BMC Bioinformatics (2015) 0.85
REGγ is associated with multiple oncogenic pathways in human cancers. BMC Cancer (2012) 0.84
Effects of RAL signal transduction in KRAS- and BRAF-mutated cells and prognostic potential of the RAL signature in colorectal cancer. Oncotarget (2015) 0.83
Specific extracellular matrix remodeling signature of colon hepatic metastases. PLoS One (2013) 0.83
Profiling post-transcriptionally networked mRNA subsets using RIP-Chip and RIP-Seq. Methods (2013) 0.81
Cardiovascular genomics: a biomarker identification pipeline. IEEE Trans Inf Technol Biomed (2012) 0.81
Layered signaling regulatory networks analysis of gene expression involved in malignant tumorigenesis of non-resolving ulcerative colitis via integration of cross-study microarray profiles. PLoS One (2013) 0.80
Identifying resistance mechanisms against five tyrosine kinase inhibitors targeting the ERBB/RAS pathway in 45 cancer cell lines. PLoS One (2013) 0.80
Dynamic classification using case-specific training cohorts outperforms static gene expression signatures in breast cancer. Int J Cancer (2014) 0.80
Clustering gene expression regulators: new approach to disease subtyping. PLoS One (2014) 0.79
ToP: a trend-of-disease-progression procedure works well for identifying cancer genes from multi-state cohort gene expression data for human colorectal cancer. PLoS One (2013) 0.79
Gene Expression Signatures Based on Variability can Robustly Predict Tumor Progression and Prognosis. Cancer Inform (2015) 0.77
t-Test at the Probe Level: An Alternative Method to Identify Statistically Significant Genes for Microarray Data. Microarrays (Basel) (2014) 0.75
Validation of RNAi Silencing Efficiency Using Gene Array Data shows 18.5% Failure Rate across 429 Independent Experiments. Mol Ther Nucleic Acids (2016) 0.75
Improving Pathological Assessment of Breast Cancer by Employing Array-Based Transcriptome Analysis. Microarrays (Basel) (2013) 0.75
The effects of lymph node status on predicting outcome in ER+ /HER2- tamoxifen treated breast cancer patients using gene signatures. BMC Cancer (2016) 0.75
A predictor for predicting Escherichia coli transcriptome and the effects of gene perturbations. BMC Bioinformatics (2014) 0.75
Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics (2003) 100.88
Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol (2002) 82.19
Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection. Proc Natl Acad Sci U S A (2001) 68.44
affy--analysis of Affymetrix GeneChip data at the probe level. Bioinformatics (2004) 32.08
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
Normalization of real-time quantitative reverse transcription-PCR data: a model-based variance estimation approach to identify genes suited for normalization, applied to bladder and colon cancer data sets. Cancer Res (2004) 25.98
Variance stabilization applied to microarray data calibration and to the quantification of differential expression. Bioinformatics (2002) 20.59
Oncogenic pathway signatures in human cancers as a guide to targeted therapies. Nature (2005) 19.56
Gene expression profiling in breast cancer: understanding the molecular basis of histologic grade to improve prognosis. J Natl Cancer Inst (2006) 14.60
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
Preferred analysis methods for Affymetrix GeneChips revealed by a wholly defined control dataset. Genome Biol (2005) 8.32
Robust estimators for expression analysis. Bioinformatics (2002) 8.30
Evaluation of gene expression measurements from commercial microarray platforms. Nucleic Acids Res (2003) 8.08
Pharmacogenomic predictor of sensitivity to preoperative chemotherapy with paclitaxel and fluorouracil, doxorubicin, and cyclophosphamide in breast cancer. J Clin Oncol (2006) 7.24
A benchmark for Affymetrix GeneChip expression measures. Bioinformatics (2004) 5.99
Stochastic models inspired by hybridization theory for short oligonucleotide arrays. J Comput Biol (2005) 5.63
Redefinition of Affymetrix probe sets by sequence overlap with cDNA microarray probes reduces cross-platform inconsistencies in cancer-associated gene expression measurements. BMC Bioinformatics (2005) 3.66
Expression profiling--best practices for data generation and interpretation in clinical trials. Nat Rev Genet (2004) 2.91
A new summarization method for Affymetrix probe level data. Bioinformatics (2006) 2.82
Gene expression levels assessed by oligonucleotide microarray analysis and quantitative real-time RT-PCR -- how well do they correlate? BMC Genomics (2005) 2.76
Comparative analysis of microarray normalization procedures: effects on reverse engineering gene networks. Bioinformatics (2007) 2.63
Evaluation of external RNA controls for the assessment of microarray performance. Nat Biotechnol (2006) 2.59
Evaluation of methods for oligonucleotide array data via quantitative real-time PCR. BMC Bioinformatics (2006) 2.35
Comparative analysis of algorithms for signal quantitation from oligonucleotide microarrays. Bioinformatics (2004) 2.04
The utility of MAS5 expression summary and detection call algorithms. BMC Bioinformatics (2007) 1.67
Gene expression profiling of 30 cancer cell lines predicts resistance towards 11 anticancer drugs at clinically achieved concentrations. Int J Cancer (2006) 1.53
A distribution free summarization method for Affymetrix GeneChip arrays. Bioinformatics (2006) 1.46
Comprehensive analysis of affymetrix exon arrays using BioConductor. PLoS Comput Biol (2008) 1.39
Correction of technical bias in clinical microarray data improves concordance with known biological information. Genome Biol (2008) 1.27
Inflammation, adenoma and cancer: objective classification of colon biopsy specimens with gene expression signature. Dis Markers (2008) 1.24
The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements. Nat Biotechnol (2006) 30.90
An online survival analysis tool to rapidly assess the effect of 22,277 genes on breast cancer prognosis using microarray data of 1,809 patients. Breast Cancer Res Treat (2009) 7.91
A signature of chromosomal instability inferred from gene expression profiles predicts clinical outcome in multiple human cancers. Nat Genet (2006) 7.16
Reliability and reproducibility issues in DNA microarray measurements. Trends Genet (2005) 6.79
Robustness of cellular functions. Cell (2004) 6.65
Efficacy of neoadjuvant Cisplatin in triple-negative breast cancer. J Clin Oncol (2010) 5.50
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
Chromosomal instability confers intrinsic multidrug resistance. Cancer Res (2011) 3.70
Redefinition of Affymetrix probe sets by sequence overlap with cDNA microarray probes reduces cross-platform inconsistencies in cancer-associated gene expression measurements. BMC Bioinformatics (2005) 3.66
A large-scale analysis of tissue-specific pathology and gene expression of human disease genes and complexes. Proc Natl Acad Sci U S A (2008) 3.57
PGC-1α, a potential therapeutic target for early intervention in Parkinson's disease. Sci Transl Med (2010) 3.48
Molecular markers of early Parkinson's disease based on gene expression in blood. Proc Natl Acad Sci U S A (2007) 3.03
DNA methylation biomarkers for blood-based colorectal cancer screening. Clin Chem (2007) 2.65
Amplification of LAPTM4B and YWHAZ contributes to chemotherapy resistance and recurrence of breast cancer. Nat Med (2010) 2.62
Sensitive detection of colorectal cancer in peripheral blood by septin 9 DNA methylation assay. PLoS One (2008) 2.46
GATA transcription factors directly regulate the Parkinson's disease-linked gene alpha-synuclein. Proc Natl Acad Sci U S A (2008) 2.17
Chromosomal instability determines taxane response. Proc Natl Acad Sci U S A (2009) 2.12
Jetset: selecting the optimal microarray probe set to represent a gene. BMC Bioinformatics (2011) 2.09
Paradoxical relationship between chromosomal instability and survival outcome in cancer. Cancer Res (2011) 2.05
Dynamic expression profile of p21WAF1/CIP1 and Ki-67 predicts survival in rectal carcinoma treated with preoperative radiochemotherapy. J Clin Oncol (2003) 2.04
Increased measurement accuracy for sequence-verified microarray probes. Physiol Genomics (2004) 1.75
A prognostic gene expression index in ovarian cancer - validation across different independent data sets. J Pathol (2009) 1.55
Gene expression profiling of 30 cancer cell lines predicts resistance towards 11 anticancer drugs at clinically achieved concentrations. Int J Cancer (2006) 1.53
Replacing cRNA targets with cDNA reduces microarray cross-hybridization. Nat Biotechnol (2006) 1.49
Lactate dehydrogenase as a selection criterion for ipilimumab treatment in metastatic melanoma. Cancer Immunol Immunother (2014) 1.42
Parallel evolution of tumour subclones mimics diversity between tumours. J Pathol (2013) 1.42
Performance of epigenetic markers SEPT9 and ALX4 in plasma for detection of colorectal precancerous lesions. PLoS One (2010) 1.40
Relationship of extreme chromosomal instability with long-term survival in a retrospective analysis of primary breast cancer. Cancer Epidemiol Biomarkers Prev (2011) 1.38
Improved cellular pharmacokinetics and pharmacodynamics underlie the wide anticancer activity of sagopilone. Cancer Res (2008) 1.29
Correction of technical bias in clinical microarray data improves concordance with known biological information. Genome Biol (2008) 1.27
Aristaless-like homeobox-4 gene methylation is a potential marker for colorectal adenocarcinomas. Gastroenterology (2006) 1.26
Targeting chromosomal instability and tumour heterogeneity in HER2-positive breast cancer. J Cell Biochem (2010) 1.25
Overexpression of cMOAT (MRP2/ABCC2) is associated with decreased formation of platinum-DNA adducts and decreased G2-arrest in melanoma cells resistant to cisplatin. J Invest Dermatol (2003) 1.23
Reversal of P-glycoprotein-mediated multidrug resistance in cancer cells by the c-Jun NH2-terminal kinase. Cancer Res (2006) 1.16
Modulation of the classical multidrug resistance (MDR) phenotype by RNA interference (RNAi). FEBS Lett (2003) 1.15
Predictive biomarker discovery through the parallel integration of clinical trial and functional genomics datasets. Genome Med (2010) 1.12
Tumor mutation burden forecasts outcome in ovarian cancer with BRCA1 or BRCA2 mutations. PLoS One (2013) 1.11
RNA interference-triggered reversal of ABCC2-dependent cisplatin resistance in human cancer cells. Biochem Biophys Res Commun (2006) 1.09
ABCC2 (MRP2, cMOAT) can be localized in the nuclear membrane of ovarian carcinomas and correlates with resistance to cisplatin and clinical outcome. Clin Cancer Res (2006) 1.08
Prognostic and predictive markers in metastatic renal cell carcinoma. J Clin Oncol (2013) 1.08
Overexpression of cathepsin B in gastric cancer identified by proteome analysis. Proteomics (2005) 1.08
Relationship between the expression of cyclooxygenase 2 and MDR1/P-glycoprotein in invasive breast cancers and their prognostic significance. Breast Cancer Res (2005) 1.07
Reversal of breast cancer resistance protein-mediated drug resistance by tryprostatin A. Int J Cancer (2003) 1.07
Augmented expression of metallothionein and glutathione S-transferase pi as unfavourable prognostic factors in cisplatin-treated ovarian cancer patients. Virchows Arch (2005) 1.06
Three-dimensional virtual microscopy of colorectal biopsies. Arch Pathol Lab Med (2005) 1.06
Protection of platinum-DNA adduct formation and reversal of cisplatin resistance by anti-MRP2 hammerhead ribozymes in human cancer cells. Int J Cancer (2005) 1.02
YB-1 relocates to the nucleus in adenovirus-infected cells and facilitates viral replication by inducing E2 gene expression through the E2 late promoter. J Biol Chem (2002) 1.01
Prediction of doxorubicin sensitivity in breast tumors based on gene expression profiles of drug-resistant cell lines correlates with patient survival. Oncogene (2005) 1.01
Enhanced exposure of phosphatidylserine in human gastric carcinoma cells overexpressing the half-size ABC transporter BCRP (ABCG2). Biochem J (2003) 1.01
Stable and complete overcoming of MDR1/P-glycoprotein-mediated multidrug resistance in human gastric carcinoma cells by RNA interference. Cancer Gene Ther (2004) 0.98
Estrogen receptor alpha expression in ovarian cancer predicts longer overall survival. Pathol Oncol Res (2011) 0.98
Expression of multidrug resistance-associated protein 1 in invasive ovarian carcinoma: implication for prognosis. Histopathology (2009) 0.97
Occurence of stromal myofibroblasts in the invasive ductal breast cancer tissue is an unfavourable prognostic factor. Anticancer Res (2007) 0.97
Minimising immunohistochemical false negative ER classification using a complementary 23 gene expression signature of ER status. PLoS One (2010) 0.97
Aberrant septin 9 DNA methylation in colorectal cancer is restricted to a single CpG island. BMC Cancer (2013) 0.97
Alterations of glutathione S-transferase and matrix metalloproteinase-9 expressions are early events in esophageal carcinogenesis. World J Gastroenterol (2007) 0.96
RNA expression of MDR1/P-glycoprotein, DNA-topoisomerase I, and MRP2 in ovarian carcinoma patients: correlation with chemotherapeutic response. Gynecol Oncol (2004) 0.96
A Web-based data warehouse on gene expression in human malignant melanoma. J Invest Dermatol (2006) 0.95
Acquired cisplatin resistance in the head-neck cancer cell line Cal27 is associated with decreased DKK1 expression and can partially be reversed by overexpression of DKK1. Int J Cancer (2008) 0.95
CD46 expression is indicative of shorter revival-free survival for ovarian cancer patients. Anticancer Res (2007) 0.94
Identification and validation of colorectal neoplasia-specific methylation markers for accurate classification of disease. Mol Cancer Res (2007) 0.94
Interleukin-1 beta and tumor necrosis factor-alpha increase ABCG2 expression in MCF-7 breast carcinoma cell line and its mitoxantrone-resistant derivative, MCF-7/MX. Inflamm Res (2009) 0.94
Study of therapy resistance in cancer cells with functional proteome analysis. Clin Chem Lab Med (2002) 0.94
The CIN4 chromosomal instability qPCR classifier defines tumor aneuploidy and stratifies outcome in grade 2 breast cancer. PLoS One (2013) 0.92
Optimization of the BLASTN substitution matrix for prediction of non-specific DNA microarray hybridization. Nucleic Acids Res (2009) 0.92
In silico prediction of tumor antigens derived from functional missense mutations of the cancer gene census. Oncoimmunology (2012) 0.92
Immunophenotypic profiling of nonsmall cell lung cancer progression using the tissue microarray approach. Appl Immunohistochem Mol Morphol (2007) 0.92
Overcoming the classical multidrug resistance phenotype by adenoviral delivery of anti-MDR1 short hairpin RNAs and ribozymes. Int J Oncol (2007) 0.91
Complete in vivo reversal of the multidrug resistance phenotype by jet-injection of anti-MDR1 short hairpin RNA-encoding plasmid DNA. Mol Ther (2007) 0.91
Nuclear metallothionein expression correlates with cisplatin resistance of ovarian cancer cells and poor clinical outcome. Virchows Arch (2007) 0.91
Influx and efflux transport as determinants of melphalan cytotoxicity: Resistance to melphalan in MDR1 overexpressing tumor cell lines. Biochem Pharmacol (2009) 0.90
Topoisomerase IIalpha mRNA and protein expression in ovarian carcinoma: correlation with clinicopathological factors and prognosis. Mod Pathol (2009) 0.90
Study of the development of chemoresistance in melanoma cell lines using proteome analysis. Electrophoresis (2003) 0.90
The gene polymorphism of the angiotensin I-converting enzyme correlates with tumor size and patient survival in colorectal cancer patients. Neoplasia (2007) 0.89
CD24 expression is specific for tamoxifen-resistant ductal breast cancer cases. Anticancer Res (2006) 0.89
Multidrug-resistant cancer cells facilitate E1-independent adenoviral replication: impact for cancer gene therapy. Cancer Res (2004) 0.89
Elevated nuclear S100P expression is associated with poor survival in early breast cancer patients. Histol Histopathol (2013) 0.89
Complete reversal of ABCG2-depending atypical multidrug resistance by RNA interference in human carcinoma cells. Oligonucleotides (2006) 0.89
Automated classification of inflammation in colon histological sections based on digital microscopy and advanced image analysis. Cytometry A (2008) 0.88
ABCC2 (MRP2, cMOAT) localized in the nuclear envelope of breast carcinoma cells correlates with poor clinical outcome. Pathol Oncol Res (2011) 0.88
Comparision of the cytotoxic effects of birch bark extract, betulin and betulinic acid towards human gastric carcinoma and pancreatic carcinoma drug-sensitive and drug-resistant cell lines. Molecules (2009) 0.87
Deconvoluting complex tissues for expression quantitative trait locus-based analyses. Philos Trans R Soc Lond B Biol Sci (2013) 0.87
Identification of differentially expressed genes in classical and atypical multidrug-resistant gastric carcinoma cells. Anticancer Res (2003) 0.87