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  1. Article ; Online: Glycoprotein analysis using protein microarrays and mass spectrometry.

    Patwa, Tasneem / Li, Chen / Simeone, Diane M / Lubman, David M

    Mass spectrometry reviews

    2010  Volume 29, Issue 5, Page(s) 830–844

    Abstract: Protein glycosylation plays an important role in a multitude of biological processes such as cell-cell recognition, growth, differentiation, and cell death. It has been shown that specific glycosylation changes are key in disease progression and can have ...

    Abstract Protein glycosylation plays an important role in a multitude of biological processes such as cell-cell recognition, growth, differentiation, and cell death. It has been shown that specific glycosylation changes are key in disease progression and can have diagnostic value for a variety of disease types such as cancer and inflammation. The complexity of carbohydrate structures and their derivatives makes their study a real challenge. Improving the isolation, separation, and characterization of carbohydrates and their glycoproteins is a subject of increasing scientific interest. With the development of new stationary phases and molecules that have affinity properties for glycoproteins, the isolation and separation of these compounds have advanced significantly. In addition to detection with mass spectrometry, the microarray platform has become an essential tool to characterize glycan structure and to study glycosylation-related biological interactions, by using probes as a means to interrogate the spotted or captured glycosylated molecules on the arrays. Furthermore, the high-throughput and reproducible nature of microarray platforms have been highlighted by its extensive applications in the field of biomarker validation, where a large number of samples must be analyzed multiple times. This review covers a brief survey of the other experimental methodologies that are currently being developed and used to study glycosylation and emphasizes methodologies that involve the use of microarray platforms. This review describes recent advances in several options of microarray platforms used in glycoprotein analysis, including glycoprotein arrays, glycan arrays, lectin arrays, and antibody/lectin arrays. The translational use of these arrays in applications related to characterization of cells and biomarker discovery is also included.
    MeSH term(s) Antibodies ; Chromatography, High Pressure Liquid/methods ; Glycoproteins/analysis ; Glycoproteins/blood ; Glycosylation ; Humans ; Lectins ; Mass Spectrometry/methods ; Neoplasms/blood ; Protein Array Analysis/methods
    Chemical Substances Antibodies ; Glycoproteins ; Lectins
    Language English
    Publishing date 2010-01-20
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 1491946-1
    ISSN 1098-2787 ; 0277-7037
    ISSN (online) 1098-2787
    ISSN 0277-7037
    DOI 10.1002/mas.20269
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: Identification of differentially expressed spatial clusters using humoral response microarray data.

    Wu, Jincao / Patwa, Tasneem H / Lubman, David M / Ghosh, Debashis

    Computational statistics & data analysis

    2009  Volume 53, Issue 8, Page(s) 3094–3102

    Abstract: ... simultaneously and is used increasingly nowadays. To study humoral response in pancreatic cancers, Patwa et al ...

    Abstract The antibody microarray is a powerful chip-based technology for profiling hundreds of proteins simultaneously and is used increasingly nowadays. To study humoral response in pancreatic cancers, Patwa et al. (2007) developed a two-dimensional liquid separation technique and built a two-dimensional antibody microarray. However, identifying differential expression regions on the antibody microarray requires the use of appropriate statistical methods to fairly assess the large amounts of data generated. In this paper, we propose a permutation-based test using spatial information of the two-dimensional antibody microarray. By borrowing strength from the neighboring differentially expressed spots, we are able to detect the differential expression region with very high power controlling type I error at 0.05 in our simulation studies. We also apply the proposed methodology to a real microarray dataset.
    Language English
    Publishing date 2009-09-17
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 1478763-5
    ISSN 0167-9473
    ISSN 0167-9473
    DOI 10.1016/j.csda.2008.04.026
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article: Protein biomarkers in cancer: natural glycoprotein microarray approaches.

    Zhao, Jia / Patwa, Tasneem H / Lubman, David M / Simeone, Diane M

    Current opinion in molecular therapeutics

    2008  Volume 10, Issue 6, Page(s) 602–610

    Abstract: Protein glycosylation is the most versatile and common protein modification and plays important roles in various biological processes and disease progression. In this review, the development of microarray technology for protein glycosylation analysis is ... ...

    Abstract Protein glycosylation is the most versatile and common protein modification and plays important roles in various biological processes and disease progression. In this review, the development of microarray technology for protein glycosylation analysis is described. Three types are discussed: carbohydrate, lectin and natural glycoprotein microarrays. The advantages of microarray technology to study protein glycosylation are high-volume throughput coupled with a highly miniaturized platform. These techniques show great promise for detecting interactions that involve carbohydrates and as a screening tool to detect glycan patterns important for the early diagnosis of disease.
    MeSH term(s) Animals ; Biomarkers, Tumor/analysis ; Biomarkers, Tumor/metabolism ; Glycoproteins/analysis ; Glycoproteins/chemistry ; Glycoproteins/metabolism ; Glycosylation ; Humans ; Lectins/analysis ; Models, Biological ; Neoplasms/diagnosis ; Neoplasms/metabolism ; Protein Array Analysis/methods
    Chemical Substances Biomarkers, Tumor ; Glycoproteins ; Lectins
    Keywords covid19
    Language English
    Publishing date 2008-12-03
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 2022273-7
    ISSN 1464-8431
    ISSN 1464-8431
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article: Glycoprotein analysis using protein microarrays and mass spectrometry

    Patwa, Tasneem / Li, Chen / Simeone, Diane M / Lubman, David M

    Mass spectrometry reviews. 2010 Sept., v. 29, no. 5

    2010  

    Abstract: Protein glycosylation plays an important role in a multitude of biological processes such as cell-cell recognition, growth, differentiation, and cell death. It has been shown that specific glycosylation changes are key in disease progression and can have ...

    Abstract Protein glycosylation plays an important role in a multitude of biological processes such as cell-cell recognition, growth, differentiation, and cell death. It has been shown that specific glycosylation changes are key in disease progression and can have diagnostic value for a variety of disease types such as cancer and inflammation. The complexity of carbohydrate structures and their derivatives makes their study a real challenge. Improving the isolation, separation, and characterization of carbohydrates and their glycoproteins is a subject of increasing scientific interest. With the development of new stationary phases and molecules that have affinity properties for glycoproteins, the isolation and separation of these compounds have advanced significantly. In addition to detection with mass spectrometry, the microarray platform has become an essential tool to characterize glycan structure and to study glycosylation-related biological interactions, by using probes as a means to interrogate the spotted or captured glycosylated molecules on the arrays. Furthermore, the high-throughput and reproducible nature of microarray platforms have been highlighted by its extensive applications in the field of biomarker validation, where a large number of samples must be analyzed multiple times. This review covers a brief survey of the other experimental methodologies that are currently being developed and used to study glycosylation and emphasizes methodologies that involve the use of microarray platforms. This review describes recent advances in several options of microarray platforms used in glycoprotein analysis, including glycoprotein arrays, glycan arrays, lectin arrays, and antibody/lectin arrays. The translational use of these arrays in applications related to characterization of cells and biomarker discovery is also included.
    Language English
    Dates of publication 2010-09
    Size p. 830-844.
    Publishing place Wiley Subscription Services, Inc., A Wiley Company
    Document type Article
    ZDB-ID 1491946-1
    ISSN 1098-2787 ; 0277-7037
    ISSN (online) 1098-2787
    ISSN 0277-7037
    DOI 10.1002/mas.20269
    Database NAL-Catalogue (AGRICOLA)

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  5. Article: Enhanced detection of autoantibodies on protein microarrays using a modified protein digestion technique.

    Patwa, Tasneem H / Wang, Yanfei / Simeone, Diane M / Lubman, David M

    Journal of proteome research

    2008  Volume 7, Issue 6, Page(s) 2553–2561

    Abstract: High-throughput studies to determine differential immune (humoral) response to diseases are becoming of increasing interest because the information they provide can help in early diagnosis as well as monitoring of therapeutics. Protein microarrays are a ... ...

    Abstract High-throughput studies to determine differential immune (humoral) response to diseases are becoming of increasing interest because the information they provide can help in early diagnosis as well as monitoring of therapeutics. Protein microarrays are a high-throughput and convenient technology that can be applied to the study of the humoral response. Proteins can be arrayed on slides and then probed with serum from different classes of patients to observe differences that may exist among autoantibodies that reflect differences in disease states. However, such studies may be difficult to interpret due to the weak overall signal response of such protein microarrays. We propose that this weak signal response is due to the physical positioning of the disease proteins that renders them sterically hindered from binding partners in the serum. In this study, we hypothesize that reducing the complexity and size of the disease proteins by chemical digestion using cyanogen bromide (CNBr) may enhance the overall signal from the humoral response and facilitate visualization of disease-specific responses in various classes of serum. A modified protein microarray methodology using CNBr digestion is presented here. The new workflow was applied to a set of 10 serum samples from healthy subjects, 10 from patients with chronic pancreatitis and 10 from patients diagnosed with pancreatic cancer and the results were compared to results obtained in the absence of CNBr digestion. CNBr digestion allowed the identification of 10 additional autoantibodies that responded to serum, 5 of which were unique to pancreatitis and cancer sera. This new methodology may increase the sensitivity of microarray studies measuring autoantibodies in serum.
    MeSH term(s) Antigen-Antibody Reactions ; Antigens/analysis ; Antigens/chemistry ; Antigens/isolation & purification ; Autoantibodies/analysis ; Autoantibodies/blood ; Autoantibodies/immunology ; Carbon-Carbon Double Bond Isomerases/analysis ; Carbon-Carbon Double Bond Isomerases/immunology ; Cell Line, Tumor ; Cyanogen Bromide/chemistry ; Humans ; Membrane Transport Proteins/analysis ; Membrane Transport Proteins/immunology ; Pancreatic Neoplasms/blood ; Pancreatic Neoplasms/immunology ; Pancreatitis, Chronic/blood ; Pancreatitis, Chronic/immunology ; Peptide Fragments/immunology ; Protein Array Analysis/methods ; Proteins/chemistry ; Proteins/immunology ; Proteins/isolation & purification ; Reproducibility of Results ; Tandem Mass Spectrometry ; Transcription Factors/analysis ; Transcription Factors/immunology ; Trypsin/chemistry ; Ubiquitin-Conjugating Enzymes/analysis ; Ubiquitin-Conjugating Enzymes/immunology
    Chemical Substances Antigens ; Autoantibodies ; Membrane Transport Proteins ; Peptide Fragments ; Proteins ; TIMM8A protein, human ; Transcription Factors ; UBE2V1 protein, human (EC 2.3.2.23) ; Ubiquitin-Conjugating Enzymes (EC 2.3.2.23) ; Trypsin (EC 3.4.21.4) ; Carbon-Carbon Double Bond Isomerases (EC 5.3.3.-) ; delta(3,5),delta(2,4)-dienoyl-CoA isomerase (EC 5.3.3.-) ; Cyanogen Bromide (OS382OHJ8P)
    Language English
    Publishing date 2008-05-02
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2078618-9
    ISSN 1535-3893
    ISSN 1535-3893
    DOI 10.1021/pr800023g
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article: Early detection and biomarkers in pancreatic cancer.

    Misek, David E / Patwa, Tasneem H / Lubman, David M / Simeone, Diane M

    Journal of the National Comprehensive Cancer Network : JNCCN

    2007  Volume 5, Issue 10, Page(s) 1034–1041

    Abstract: Major advances in cancer control will be greatly aided by early detection for diagnosing and treating cancer in its preinvasive state before metastasis. Unfortunately, for pancreatic ductal adenocarcinoma (PDAC), which is the fourth leading cause of ... ...

    Abstract Major advances in cancer control will be greatly aided by early detection for diagnosing and treating cancer in its preinvasive state before metastasis. Unfortunately, for pancreatic ductal adenocarcinoma (PDAC), which is the fourth leading cause of cancer-related death in the United States, effective early detection and screening are currently not available and tumors are typically diagnosed at a late stage, frequently after metastasis. Partly because of low sensitivity/specificity, existing biomarkers such as CA19-9 are not adequate as early detection markers of pancreatic cancer. Thus, a great need exists for new biomarkers for pancreatic cancer. This article focuses on recent developments in the identification of new serum protein biomarkers that are useful in the early detection of PDAC.
    MeSH term(s) Adenocarcinoma/diagnosis ; Adenocarcinoma/immunology ; Antibody Formation ; Biomarkers, Tumor/analysis ; Humans ; Mass Spectrometry ; Neoplasm Proteins/analysis ; Pancreatic Neoplasms/diagnosis ; Pancreatic Neoplasms/immunology ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
    Chemical Substances Biomarkers, Tumor ; Neoplasm Proteins
    Language English
    Publishing date 2007-09-14
    Publishing country United States
    Document type Journal Article ; Review
    ZDB-ID 2250759-0
    ISSN 1540-1405
    ISSN 1540-1405
    DOI 10.6004/jnccn.2007.0086
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article: All-liquid separations, protein microarrays, and mass spectrometry to interrogate serum proteomes: an application to serum glycoproteomics.

    Patwa, Tasneem H / Qiu, Yinghua / Zhao, Jia / Simeone, Diane M / Lubman, David M

    Methods in molecular biology (Clifton, N.J.)

    2009  Volume 520, Page(s) 75–87

    Abstract: Disease-related changes in serum proteins are reasonable targets for early detection particularly due to the noninvasive approach in obtaining samples. Glycoproteins specifically have been implicated in a variety of disease types ranging from immune ... ...

    Abstract Disease-related changes in serum proteins are reasonable targets for early detection particularly due to the noninvasive approach in obtaining samples. Glycoproteins specifically have been implicated in a variety of disease types ranging from immune diseases to cancers. High-throughput screening methods that can assess glycosylation states of all serum proteins in normal and diseased sample groups can facilitate early detection as well as shed light on disease progression mechanisms. Outlined here is a combination of liquid separation, protein microarray, and mass spectrometry approach to highlight candidate proteins involved in diseases through glycosylation mechanisms.
    MeSH term(s) Blood Proteins/analysis ; Chromatography, High Pressure Liquid ; Electrophoresis, Polyacrylamide Gel ; Glycoproteins/blood ; Glycosylation ; Humans ; Lectins/isolation & purification ; Mass Spectrometry ; Membranes, Artificial ; Peptide Mapping ; Porosity ; Protein Array Analysis/methods ; Proteome/analysis ; Proteomics/methods ; Trypsin/metabolism
    Chemical Substances Blood Proteins ; Glycoproteins ; Lectins ; Membranes, Artificial ; Proteome ; Trypsin (EC 3.4.21.4)
    Language English
    Publishing date 2009
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ISSN 1064-3745
    ISSN 1064-3745
    DOI 10.1007/978-1-60327-811-9_6
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article: Analysis of protein glycosylation and phosphorylation using liquid phase separation, protein microarray technology, and mass spectrometry.

    Zhao, Jia / Patwa, Tasneem H / Pal, Manoj / Qiu, Weilian / Lubman, David M

    Methods in molecular biology (Clifton, N.J.)

    2009  Volume 492, Page(s) 321–351

    Abstract: Protein glycosylation and phosphorylation are very common posttranslational modifications. The alteration of these modifications in cancer cells is closely related to the onset and progression of cancer and other disease states. In this protocol, ... ...

    Abstract Protein glycosylation and phosphorylation are very common posttranslational modifications. The alteration of these modifications in cancer cells is closely related to the onset and progression of cancer and other disease states. In this protocol, strategies for monitoring the changes in protein glycosylation and phosphorylation in serum or tissue cells on a global scale and specifically characterizing these alterations are included. The technique is based on lectin affinity enrichment for glycoproteins, all liquid-phase two-dimensional fractionation, protein microarray, and mass spectrometry technology. Proteins are separated based on pI in the first dimension using chromatofocusing (CF) or liquid isoelectric focusing (IEF) followed by the second-dimension separation using nonporous silica RP-HPLC. Five lectins with different binding specificities to glycan structures are used for screening glycosylation patterns in human serum through a biotin streptavidin system. Fluorescent phosphodyes and phosphospecific antibodies are employed to detect specific phosphorylated proteins in cell lines or human tissues. The purified proteins of interest are identified by peptide sequencing. Their modifications including glycosylation and phosphorylation could be further characterized by mass-spectrometry-based approaches. These strategies can be used in biological samples for large-scale glycoproteome/phosphoproteome screening as well as for individual protein modification analysis.
    MeSH term(s) Amino Acid Sequence ; Analytic Sample Preparation Methods ; Animals ; Biomarkers, Tumor/analysis ; Biomarkers, Tumor/chemistry ; Biomarkers, Tumor/isolation & purification ; Biomarkers, Tumor/metabolism ; Blood Proteins/analysis ; Blood Proteins/chemistry ; Blood Proteins/isolation & purification ; Blood Proteins/metabolism ; Cattle ; Cell Line, Tumor ; Chemical Fractionation ; Chromatography, Affinity ; Chromatography, High Pressure Liquid ; Glycosylation ; Humans ; Hydrophobic and Hydrophilic Interactions ; Immunoglobulins/immunology ; Lectins ; Mass Spectrometry/methods ; Molecular Sequence Data ; Phosphoproteins/analysis ; Phosphoproteins/chemistry ; Phosphoproteins/isolation & purification ; Phosphoproteins/metabolism ; Phosphorylation ; Protein Array Analysis/methods ; Proteomics ; Sequence Analysis, Protein
    Chemical Substances Biomarkers, Tumor ; Blood Proteins ; IgY ; Immunoglobulins ; Lectins ; Phosphoproteins
    Language English
    Publishing date 2009-02-25
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ISSN 1064-3745
    ISSN 1064-3745
    DOI 10.1007/978-1-59745-493-3_20
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article: Differential expression of acidic proteins with progression in the MCF10 model of human breast disease.

    Buchanan, Nathan S / Zhao, Jia / Zhu, Kan / Patwa, Tasneem H / Miller, Fred R / Lubman, David M

    International journal of oncology

    2007  Volume 31, Issue 4, Page(s) 941–949

    Abstract: A proteomic characterization of one premalignant (MCF10AT1) and two malignant (MCF10CA1a and MCF10 CA1d) human breast cancer cell lines has been performed using a combination of two-dimensional liquid separations and mass spectrometry. Chromatofocusing ( ... ...

    Abstract A proteomic characterization of one premalignant (MCF10AT1) and two malignant (MCF10CA1a and MCF10 CA1d) human breast cancer cell lines has been performed using a combination of two-dimensional liquid separations and mass spectrometry. Chromatofocusing (CF) and NPS-RP-HPLC are combined with ESI-TOF-MS to resolve and detect intact proteins. Simultaneously, fractions are collected and digested for protein identification using MALDI-MS peptide mass fingerprinting. Following protein identification a small database was compiled for use in comparison between IDs and measured masses taking into account variables such as pI, hydrophobicity and potential modifications. Out of 239 mass bands detected between pH 4.6 and 6.0, 133 have been definitively associated with identified proteins and 67 show consistent up/down regulation in two malignant breast cancer cell lines relative to the precursor premalignant cell line. Of these, 8 are also altered in the premalignant MCF10AT1 cell line by treatment with estradiol. Differentially expressed proteins indicate significant changes to the cytoskeleton, cellular metabolism, and adaptation to environmental stressors in malignant cell lines.
    MeSH term(s) Biomarkers, Tumor/metabolism ; Breast Neoplasms/metabolism ; Chromatography, High Pressure Liquid ; Disease Progression ; Electrophoresis, Gel, Two-Dimensional ; Humans ; Isoelectric Focusing ; Neoplasm Proteins/metabolism ; Peptide Mapping ; Proteome/analysis ; Spectrometry, Mass, Electrospray Ionization ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
    Chemical Substances Biomarkers, Tumor ; Neoplasm Proteins ; Proteome
    Language English
    Publishing date 2007-10
    Publishing country Greece
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 1154403-x
    ISSN 1019-6439
    ISSN 1019-6439
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: The identification of auto-antibodies in pancreatic cancer patient sera using a naturally fractionated Panc-1 cell line.

    Li, Chen / Kim, Hye-Yeung / Vuong, Huy / Patwa, Tasneem / Pal, Manoj / Brand, Randall E / Simeone, Diane M / Lubman, David M

    Cancer biomarkers : section A of Disease markers

    2010  Volume 7, Issue 1, Page(s) 25–37

    Abstract: The immunogenic nature of cancer can be explored to distinguish pancreatic cancer from related non-cancer conditions. We describe a liquid-based microarray approach followed by statistical analysis and confirmation for discovery of auto-immune biomarkers ...

    Abstract The immunogenic nature of cancer can be explored to distinguish pancreatic cancer from related non-cancer conditions. We describe a liquid-based microarray approach followed by statistical analysis and confirmation for discovery of auto-immune biomarkers for pancreatic cancer. Proteins from the Panc-1 pancreatic cancer cell line were fractionated using a 2-D liquid separation method into over 1052 fractions and spotted onto nitrocellulose coated glass slides. The slides were hybridized with 37 pancreatic cancer sera, 24 chronic pancreatitis sera and 23 normal sera to detect elevated levels of reactivity against the proteins in spotted fractions. The response data obtained from protein microarrays was first analyzed by Wilcoxon Rank-Sum Tests to generate two lists of fractions that positively responded to the cancer sera and showed p-values less than 0.02 in the pairwise comparison between cancer specimens and normal and chronic pancreatitis specimens. The top 3 fractions with the lowest correlations were combined in receiver operating characteristic analyses. The area-under-the-curve (AUC) values are 0.813 and 0.792 for cancer vs. normal and cancer vs. pancreatitis respectively. Outlier-Sum statistics were then applied to the microarray data to determine the existence of outliers exclusive in cancer sera. The selected fractions were identified by LC-MS/MS. We further confirmed the occurrence of outliers with three proteins among cancer samples in a confirmation experiment using a separate dataset of 165 serum samples containing 48 cancer sera and 117 non-cancer controls. Phosphoglycerate kinase 1 (PGK1) elicited greater reactivity in 20.9% (10 in 48) of the samples in the cancer group, while no outlier was present in the non-cancer groups.
    MeSH term(s) Aged ; Antibodies, Neoplasm/blood ; Autoantibodies/blood ; Cell Line, Tumor ; Humans ; Middle Aged ; Pancreas/immunology ; Pancreatic Neoplasms/immunology ; Pancreatitis/immunology ; Phosphoglycerate Kinase/blood ; Protein Array Analysis/methods ; ROC Curve
    Chemical Substances Antibodies, Neoplasm ; Autoantibodies ; Phosphoglycerate Kinase (EC 2.7.2.3)
    Language English
    Publishing date 2010-11-02
    Publishing country Netherlands
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2203517-5
    ISSN 1875-8592 ; 1574-0153 ; 1875-8592
    ISSN (online) 1875-8592 ; 1574-0153
    ISSN 1875-8592
    DOI 10.3233/CBM-2010-0145
    Database MEDical Literature Analysis and Retrieval System OnLINE

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