Dual-color proteomic profiling of complex samples with a microarray of 810 cancer-related antibodies.

PubWeight™: 1.21‹?› | Rank: Top 10%

🔗 View Article (PMC 2877986)

Published in Mol Cell Proteomics on February 16, 2010

Authors

Christoph Schröder1, Anette Jacob, Sarah Tonack, Tomasz P Radon, Martin Sill, Manuela Zucknick, Sven Rüffer, Eithne Costello, John P Neoptolemos, Tatjana Crnogorac-Jurcevic, Andrea Bauer, Kurt Fellenberg, Jörg D Hoheisel

Author Affiliations

1: Division of Functional Genome Analysis, Deutsches Krebsforschungszentrum, 69120 Heidelberg, Germany. christoph.schroeder@dkfz.de

Articles citing this

Antibody-based proteomics: fast-tracking molecular diagnostics in oncology. Nat Rev Cancer (2010) 1.54

Profiling cellular protein complexes by proximity ligation with dual tag microarray readout. PLoS One (2012) 1.47

Diagnosis of pancreatic ductal adenocarcinoma and chronic pancreatitis by measurement of microRNA abundance in blood and tissue. PLoS One (2012) 1.36

Highly skewed distribution of miRNAs and proteins between colorectal cancer cells and their exosomes following Cetuximab treatment: biomolecular, genetic and translational implications. Oncoscience (2014) 0.97

Variance decomposition of protein profiles from antibody arrays using a longitudinal twin model. Proteome Sci (2011) 0.96

Pancreatic cancer in 2010: new insights for early intervention and detection. Nat Rev Gastroenterol Hepatol (2011) 0.94

Spatiotemporal proteomic analyses during pancreas cancer progression identifies serine/threonine stress kinase 4 (STK4) as a novel candidate biomarker for early stage disease. Mol Cell Proteomics (2014) 0.83

Assessment and optimisation of normalisation methods for dual-colour antibody microarrays. BMC Bioinformatics (2010) 0.81

Proteomics-based dissection of human endoderm progenitors by differential cell capture on antibody array. Mol Cell Proteomics (2012) 0.80

Protein analytical assays for diagnosing, monitoring, and choosing treatment for cancer patients. J Healthc Eng (2012) 0.79

Screening technologies for target identification in pancreatic cancer. Cancers (Basel) (2010) 0.77

Proteome variations in pancreatic stellate cells upon stimulation with proinflammatory factors. J Biol Chem (2013) 0.77

Clinical proteomics: promises, challenges and limitations of affinity arrays. Proteomics Clin Appl (2015) 0.77

Relative quantification of several plasma proteins during liver transplantation surgery. J Biomed Biotechnol (2011) 0.77

Protein Profiling Gastric Cancer and Neighboring Control Tissues Using High-Content Antibody Microarrays. Microarrays (Basel) (2016) 0.75

Contributions of immunoaffinity chromatography to deep proteome profiling of human biofluids. J Chromatogr B Analyt Technol Biomed Life Sci (2016) 0.75

Comparison of the tumor cell secretome and patient sera for an accurate serum-based diagnosis of pancreatic ductal adenocarcinoma. Oncotarget (2017) 0.75

Proteomics in pancreatic cancer research. Int J Proteomics (2011) 0.75

Technical Advances of the Recombinant Antibody Microarray Technology Platform for Clinical Immunoproteomics. PLoS One (2016) 0.75

The Statistical Value of Raw Fluorescence Signal in Luminex xMAP Based Multiplex Immunoassays. Sci Rep (2016) 0.75

Antibody Array Revealed PRL-3 Affects Protein Phosphorylation and Cytokine Secretion. PLoS One (2017) 0.75

Articles cited by this

Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol (2004) 101.91

The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements. Nat Biotechnol (2006) 30.90

Normalization of cDNA microarray data. Methods (2003) 18.69

Use of within-array replicate spots for assessing differential expression in microarray experiments. Bioinformatics (2005) 10.64

A comparison of background correction methods for two-colour microarrays. Bioinformatics (2007) 8.59

Transcriptional gene expression profiles of colorectal adenoma, adenocarcinoma, and normal tissue examined by oligonucleotide arrays. Cancer Res (2001) 4.50

Mining the plasma proteome for cancer biomarkers. Nature (2008) 4.10

A solvent system for delipidation of plasma or serum without protein precipitation. J Lipid Res (1976) 3.24

Correspondence analysis applied to microarray data. Proc Natl Acad Sci U S A (2001) 3.19

Clinical proteomics: A need to define the field and to begin to set adequate standards. Proteomics Clin Appl (2007) 2.84

Antibodypedia, a portal for sharing antibody and antigen validation data. Mol Cell Proteomics (2008) 2.34

ProteomeBinders: planning a European resource of affinity reagents for analysis of the human proteome. Nat Methods (2007) 2.04

Reproducibility and correlations of multiplex cytokine levels in asymptomatic persons. Cancer Epidemiol Biomarkers Prev (2008) 1.96

Towards a human proteome atlas: high-throughput generation of mono-specific antibodies for tissue profiling. Proteomics (2005) 1.87

Label-free detection of differential protein expression by LC/MALDI mass spectrometry. J Proteome Res (2008) 1.78

Antibody microarray profiling reveals individual and combined serum proteins associated with pancreatic cancer. Cancer Res (2005) 1.55

Proteomic contributions to personalized cancer care. Mol Cell Proteomics (2008) 1.46

Detection of pancreatic cancer using antibody microarray-based serum protein profiling. Proteomics (2008) 1.38

Ligand assays: from electrophoresis to miniaturized microarrays. Clin Chem (1998) 1.32

Albumin depletion of human plasma also removes low abundance proteins including the cytokines. Proteomics (2005) 1.31

Antibody arrays: technical considerations and clinical applications in cancer. Clin Chem (2006) 1.26

Antibodies: The generation game. Nature (2007) 1.21

Characterization of the human blood plasma proteome. Proteomics (2005) 1.18

Optimal design of microarray immunoassays to compensate for kinetic limitations: theory and experiment. Mol Cell Proteomics (2006) 1.18

Design of high-density antibody microarrays for disease proteomics: key technological issues. J Proteomics (2009) 1.08

Optimized normalization for antibody microarrays and application to serum-protein profiling. Mol Cell Proteomics (2005) 1.08

Proteomic methodological recommendations for studies involving human plasma, platelets, and peripheral blood mononuclear cells. J Proteome Res (2008) 1.06

Assessment of albumin removal from an immunoaffinity spin column: critical implications for proteomic examination of the albuminome and albumin-depleted samples. Proteomics (2009) 1.05

A technically detailed and pragmatic protocol for quantitative serum proteomics using iTRAQ. J Proteomics (2009) 1.04

Analysis of the urine proteome in patients with pancreatic ductal adenocarcinoma. Proteomics Clin Appl (2008) 1.03

Use of high density antibody arrays to validate and discover cancer serum biomarkers. Mol Oncol (2007) 1.02

Confounding effect of obstructive jaundice in the interpretation of proteomic plasma profiling data for pancreatic cancer. J Proteome Res (2009) 1.02

Proteomics from the clinical perspective: many hopes and much debate. Nat Methods (2007) 1.01

Design of recombinant antibody microarrays for complex proteome analysis: choice of sample labeling-tag and solid support. Proteomics (2007) 1.01

Antibody microarray-based profiling of complex specimens: systematic evaluation of labeling strategies. Proteomics (2007) 0.97

"Omics" data and levels of evidence for biomarker discovery. Genomics (2008) 0.97

Proteomic analysis of human plasma proteins by two-dimensional gel electrophoresis and by antibody arrays following depletion of high-abundance proteins. Cell Biochem Biophys (2007) 0.96

Depletion of the high-abundance plasma proteins. Amino Acids (2004) 0.95

Specialized DNA arrays for the differentiation of pancreatic tumors. Clin Cancer Res (2005) 0.94

Oncoproteomic profiling with antibody microarrays. Genome Med (2009) 0.92

Quantitative proteomics and biomarker discovery in human cancer. Expert Rev Proteomics (2009) 0.92

Real-time evaluation of experimental variation in large-scale LC-MS/MS-based quantitative proteomics of complex samples. J Chromatogr B Analyt Technol Biomed Life Sci (2008) 0.86

Identification of malignancy factors by analyzing cystic tumors of the pancreas. Pancreatology (2008) 0.85

Systematic interpretation of microarray data using experiment annotations. BMC Genomics (2006) 0.83

Transferring proteomic discoveries into clinical practice. Expert Rev Proteomics (2009) 0.82

One-step fractionation of complex proteomes enables detection of low abundant analytes using antibody-based microarrays. J Proteome Res (2006) 0.79

Articles by these authors

Microarray data representation, annotation and storage. Adv Biochem Eng Biotechnol (2002) 11.13

Hotspot mutations in H3F3A and IDH1 define distinct epigenetic and biological subgroups of glioblastoma. Cancer Cell (2012) 6.71

Delayed gastric emptying (DGE) after pancreatic surgery: a suggested definition by the International Study Group of Pancreatic Surgery (ISGPS). Surgery (2007) 6.62

Phase III randomized comparison of gemcitabine versus gemcitabine plus capecitabine in patients with advanced pancreatic cancer. J Clin Oncol (2009) 5.11

IDH1 and IDH2 mutations are frequent genetic alterations in acute myeloid leukemia and confer adverse prognosis in cytogenetically normal acute myeloid leukemia with NPM1 mutation without FLT3 internal tandem duplication. J Clin Oncol (2010) 4.72

Postpancreatectomy hemorrhage (PPH): an International Study Group of Pancreatic Surgery (ISGPS) definition. Surgery (2007) 4.72

Circulating microRNAs as potential markers of human drug-induced liver injury. Hepatology (2011) 4.06

Efficacy of stapler versus hand-sewn closure after distal pancreatectomy (DISPACT): a randomised, controlled multicentre trial. Lancet (2011) 3.54

IAP Guidelines for the Surgical Management of Acute Pancreatitis. Pancreatology (2002) 3.48

BRCA2 germline mutations in familial pancreatic carcinoma. J Natl Cancer Inst (2003) 3.37

Delineation of two clinically and molecularly distinct subgroups of posterior fossa ependymoma. Cancer Cell (2011) 3.11

Preoperative platelet-lymphocyte ratio is an independent significant prognostic marker in resected pancreatic ductal adenocarcinoma. Am J Surg (2008) 2.82

Clinical and genetic characteristics of hereditary pancreatitis in Europe. Clin Gastroenterol Hepatol (2004) 2.82

Meta-analyses of chemotherapy for locally advanced and metastatic pancreatic cancer. J Clin Oncol (2007) 2.80

Optimal duration and timing of adjuvant chemotherapy after definitive surgery for ductal adenocarcinoma of the pancreas: ongoing lessons from the ESPAC-3 study. J Clin Oncol (2014) 2.64

Biology and management of pancreatic cancer. Gut (2007) 2.53

Impact of IDH1 R132 mutations and an IDH1 single nucleotide polymorphism in cytogenetically normal acute myeloid leukemia: SNP rs11554137 is an adverse prognostic factor. J Clin Oncol (2010) 2.38

Fatty acid ethyl esters cause pancreatic calcium toxicity via inositol trisphosphate receptors and loss of ATP synthesis. Gastroenterology (2006) 2.23

PPARdelta and PGC1alpha act cooperatively to induce haem oxygenase-1 and enhance vascular endothelial cell resistance to stress. Cardiovasc Res (2009) 2.20

Toward the blood-borne miRNome of human diseases. Nat Methods (2011) 2.14

Tumor recurrence and survival in patients treated for thymomas and thymic squamous cell carcinomas: a retrospective analysis. J Clin Oncol (2004) 2.11

Characterization of gene expression profiles in intraductal papillary-mucinous tumors of the pancreas. Am J Pathol (2002) 2.08

Reactive oxygen species induced by bile acid induce apoptosis and protect against necrosis in pancreatic acinar cells. Gastroenterology (2011) 2.06

ProteomeBinders: planning a European resource of affinity reagents for analysis of the human proteome. Nat Methods (2007) 2.04

Interventions for mycosis fungoides. Cochrane Database Syst Rev (2012) 1.99

Genome-wide analysis of the response to cell wall mutations in the yeast Saccharomyces cerevisiae. J Biol Chem (2003) 1.99

The impact of therapy-related acute myeloid leukemia (AML) on outcome in 2853 adult patients with newly diagnosed AML. Blood (2010) 1.96

Influence of resection margins and treatment on survival in patients with pancreatic cancer: meta-analysis of randomized controlled trials. Arch Surg (2008) 1.93

Direct activation of cytosolic Ca2+ signaling and enzyme secretion by cholecystokinin in human pancreatic acinar cells. Gastroenterology (2008) 1.89

Molecular alterations in pancreatic carcinoma: expression profiling shows that dysregulated expression of S100 genes is highly prevalent. J Pathol (2003) 1.83

Epigenetically deregulated microRNA-375 is involved in a positive feedback loop with estrogen receptor alpha in breast cancer cells. Cancer Res (2010) 1.82

Minimal access retroperitoneal pancreatic necrosectomy: improvement in morbidity and mortality with a less invasive approach. Ann Surg (2010) 1.79

Palladin mutation causes familial pancreatic cancer and suggests a new cancer mechanism. PLoS Med (2006) 1.73

Transcriptome analysis of differentiating trypanosomes reveals the existence of multiple post-transcriptional regulons. BMC Genomics (2009) 1.68

Targeted next-generation sequencing by specific capture of multiple genomic loci using low-volume microfluidic DNA arrays. Anal Bioanal Chem (2008) 1.68

Analysis of gene expression in cancer cell lines identifies candidate markers for pancreatic tumorigenesis and metastasis. Int J Cancer (2004) 1.68

Advances in counselling and surveillance of patients at risk for pancreatic cancer. Gut (2007) 1.68

Heat shock causes a decrease in polysomes and the appearance of stress granules in trypanosomes independently of eIF2(alpha) phosphorylation at Thr169. J Cell Sci (2008) 1.64

Circulating miRNAs as surrogate markers for circulating tumor cells and prognostic markers in metastatic breast cancer. Clin Cancer Res (2012) 1.63

Common genetic variants in the CLDN2 and PRSS1-PRSS2 loci alter risk for alcohol-related and sporadic pancreatitis. Nat Genet (2012) 1.63

Circulating microRNAs in plasma as early detection markers for breast cancer. Int J Cancer (2012) 1.61

Proteomic analysis of chronic pancreatitis and pancreatic adenocarcinoma. Gastroenterology (2005) 1.61

A pilot study on the application of statistical classification procedures to molecular epidemiological data. Toxicol Lett (2004) 1.60

New biomarkers and targets in pancreatic cancer and their application to treatment. Nat Rev Gastroenterol Hepatol (2012) 1.57

Quantitative DNA methylation analysis identifies a single CpG dinucleotide important for ZAP-70 expression and predictive of prognosis in chronic lymphocytic leukemia. J Clin Oncol (2012) 1.56

Pancreatic Expression database: a generic model for the organization, integration and mining of complex cancer datasets. BMC Genomics (2007) 1.56

Pancreatic cancer hENT1 expression and survival from gemcitabine in patients from the ESPAC-3 trial. J Natl Cancer Inst (2013) 1.54

Body-modifying concepts and dermatologic problems: tattooing and piercing. Clin Dermatol (2008) 1.49

Monitoring the switch from housekeeping to pathogen defense metabolism in Arabidopsis thaliana using cDNA arrays. J Biol Chem (2001) 1.45

Comprehensive analysis of matrix metalloproteinase and tissue inhibitor expression in pancreatic cancer: increased expression of matrix metalloproteinase-7 predicts poor survival. Clin Cancer Res (2004) 1.44

Intrinsic chemoresistance to gemcitabine is associated with decreased expression of BNIP3 in pancreatic cancer. Clin Cancer Res (2005) 1.44

Integrated DNA methylation and copy-number profiling identify three clinically and biologically relevant groups of anaplastic glioma. Acta Neuropathol (2014) 1.42

Ethanol toxicity in pancreatic acinar cells: mediation by nonoxidative fatty acid metabolites. Proc Natl Acad Sci U S A (2004) 1.42

Understanding metastasis in pancreatic cancer: a call for new clinical approaches. Cell (2012) 1.40

Scientific data from clinical trials: investigators' responsibilities and rights. Surg Endosc (2002) 1.39

Nrf2 is overexpressed in pancreatic cancer: implications for cell proliferation and therapy. Mol Cancer (2011) 1.38

Microarray data warehouse allowing for inclusion of experiment annotations in statistical analysis. Bioinformatics (2002) 1.37

Diagnosis of pancreatic ductal adenocarcinoma and chronic pancreatitis by measurement of microRNA abundance in blood and tissue. PLoS One (2012) 1.36

Molecular prognostic markers in pancreatic cancer. J Hepatobiliary Pancreat Surg (2002) 1.35

Solid supports for microarray immunoassays. J Mol Recognit (2003) 1.33

Monosomal karyotype in adult acute myeloid leukemia: prognostic impact and outcome after different treatment strategies. Blood (2011) 1.30

Generation of high density protein microarrays by cell-free in situ expression of unpurified PCR products. Mol Cell Proteomics (2006) 1.28

Antibody microarrays: an evaluation of production parameters. Proteomics (2003) 1.28

AGR2 is a novel surface antigen that promotes the dissemination of pancreatic cancer cells through regulation of cathepsins B and D. Cancer Res (2011) 1.26

Prognosis of resected ampullary adenocarcinoma by preoperative serum CA19-9 levels and platelet-lymphocyte ratio. J Gastrointest Surg (2008) 1.26

Alterations in cardiac DNA methylation in human dilated cardiomyopathy. EMBO Mol Med (2013) 1.23

Glucose triggers different global responses in yeast, depending on the strength of the signal, and transiently stabilizes ribosomal protein mRNAs. Mol Microbiol (2003) 1.22

Classification of R1 resections for pancreatic cancer: the prognostic relevance of tumour involvement within 1 mm of a resection margin. Histopathology (2009) 1.22

Characterization of antirrhinum petal development and identification of target genes of the class B MADS box gene DEFICIENS. Plant Cell (2004) 1.19

High nuclear S100A6 (Calcyclin) is significantly associated with poor survival in pancreatic cancer patients. Cancer Res (2005) 1.18

Extensive promoter DNA hypermethylation and hypomethylation is associated with aberrant microRNA expression in chronic lymphocytic leukemia. Cancer Res (2012) 1.18

Optimal design of microarray immunoassays to compensate for kinetic limitations: theory and experiment. Mol Cell Proteomics (2006) 1.18

Cardiac ankyrin repeat protein, a negative regulator of cardiac gene expression, is augmented in human heart failure. Biochem Biophys Res Commun (2002) 1.17

Targeted resequencing for analysis of clonal composition of recurrent gene mutations in chronic lymphocytic leukaemia. Br J Haematol (2013) 1.16

Evaluation of the 4q32-34 locus in European familial pancreatic cancer. Cancer Epidemiol Biomarkers Prev (2006) 1.16

Induction of the cytoprotective enzyme heme oxygenase-1 by statins is enhanced in vascular endothelium exposed to laminar shear stress and impaired by disturbed flow. J Biol Chem (2009) 1.16

Systemic inflammatory response predicts prognosis in patients with advanced-stage colorectal cancer. Clin Colorectal Cancer (2008) 1.15

High-dimensional Cox models: the choice of penalty as part of the model building process. Biom J (2010) 1.15

Acute pancreatitis and organ failure: pathophysiology, natural history, and management strategies. Curr Gastroenterol Rep (2004) 1.15

Application of laser capture microdissection combined with two-dimensional electrophoresis for the discovery of differentially regulated proteins in pancreatic ductal adenocarcinoma. Proteomics (2003) 1.14

The genome structure of Pseudomonas putida: high-resolution mapping and microarray analysis. Environ Microbiol (2002) 1.13

Kinetics of antigen binding to antibody microspots: strong limitation by mass transport to the surface. Proteomics (2006) 1.13

Aberrant DNA methylation characterizes juvenile myelomonocytic leukemia with poor outcome. Blood (2011) 1.12