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COMPUTER 2024年第9期57卷 96-100页

作者： Hsu, D. Frank Kristal, Bruce S. Schweikert, Christina Fordham Univ Sci New York NY 10023 USA Fordham Univ Comp & Informat Sci New York NY 10023 USA Tufts Univ Jean Mayer US Dept Agr Human Nutr Res Ctr Aging Boston MA 02111 USA St Johns Univ Comp Sci Queens NY 11439 USA St Johns Univ Data Sci Program Queens NY 11439 USA

Combinatorial fusion analysis is a paradigm that seeks to provide methods and workflows for combining multiple scoring systems in computational learning and modeling, informatics, and intelligent systems.

关键词： Combinatorial Mathematics Computational Modeling Intelligent Systems Data Models Diversity Reception Informatics Encoding MCDM Large Language Models Modeling Neural Network Drug Discovery Deep Learning Computational Model Scoring System Scoring Function Informatics Workspace Recent Example Intelligent Systems Information Retrieval Virtual Screening Euclidean Space Combination Of Algorithms Protein Structure Prediction Information Fusion Global Space gene expression microarray analysis Ranking Function Motif Detection System A Artificial Neural Network Information Bits Weak Order Ranking System Ranking Score Binary Classification

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Molecular fixative enables expression microarray analysis of microdissected clinical cervical specimens

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EXPERIMENTAL AND MOLECULAR PATHOLOGY 2014年第2期96卷 168-177页

作者： Li, Gerald van Niekerk, Dirk Miller, Dianne Ehlen, Thomas Garnis, Cathie Follen, Michele Guillaud, Martial MacAulay, Calum BC Canc Res Ctr Integrat Oncol Dept Vancouver BC V5Z 1L3 Canada BC Canc Agcy Dept Pathol & Lab Med Vancouver BC Canada Univ British Columbia Dept Obstet & Gynaecol Diamond Hlth Care Ctr Vancouver BC V5Z 1M9 Canada Texas Tech Univ Hlth Sci Ctr El Paso Paul L Foster Sch Med Laura Bush Res Inst El Paso TX USA

Formalin-fixed tissue has been a mainstay of clinical pathology laboratories, but formalin alters many biomolecules, including nucleic acids and proteins. Meanwhile, frozen tissues contain better-preserved biomolecules, but tissue morphology is affected, limiting their diagnostic utility. Molecular fixatives promise to bridge this gap by simultaneously preserving morphology and biomolecules, enabling clinical diagnosis and molecular analyses on the same specimen. While previous reports have broadly evaluated the use of molecular fixative in various human tissues, we present here the first detailed assessment of the applicability of molecular fixative to both routine histopathological diagnosis and molecular analysis of cervical tissues. Ten specimens excised via the loop electrosurgical excision procedure, which removes conical tissue samples from the cervix, were cut into alternating pieces preserved in either formalin or molecular fixative. Cervical specimens preserved in molecular fixative were easily interpretable, despite featuring more eosinophilic cytoplasm and more recognizable chromatin texture than formalin-fixed specimens. Immunohistochemical staining patterns of p16 and Ki-67 were similar between fixatives, although Ki-67 staining was stronger in the molecular fixative specimens. The RNA of molecular fixative specimens from seven cases representing various dysplasia grades was assessed for utility in expression microarray analysis. Cluster analysis and scatter plots of duplicate samples suggest that data of sufficient quality can be obtained from as little as 50 ng of RNA from molecular fixative samples. Taken together, our results show that molecular fixative may be a more versatile substitute for formalin, simultaneously preserving tissue morphology for clinical diagnosis and biomolecules for immunohistochemistry and gene expression analysis. (C) 2014 Elsevier Inc. All rights reserved.

关键词： Cervical intraepithelial neoplasia gene expression microarray analysis Immunohistochemistry Microdissection Molecular fixative

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generation of tumor-initiating cells by exogenous delivery of OCT4 transcription factor

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BREAST CANCER RESEARCH 2011年第5期13卷 R94-R94页

作者： Beltran, Adriana S. Rivenbark, Ashley G. Richardson, Bryan T. Yuan, Xinni Quian, Haili Hunt, John P. Zimmerman, Eric Graves, Lee M. Blancafort, Pilar Univ N Carolina Dept Pharmacol Chapel Hill NC 27599 USA Univ N Carolina UNC Lineberger Comprehens Canc Ctr Chapel Hill NC 27599 USA Univ N Carolina Dept Biochem & Biophys Chapel Hill NC 27599 USA Chinese Acad Med Sci State Key Lab Mol Oncol Canc Inst Hosp Beijing 100021 Peoples R China Univ N Carolina Dept Pathol & Lab Med Chapel Hill NC 27599 USA

Introduction: Tumor-initiating cells (TIC) are being extensively studied for their role in tumor etiology, maintenance and resistance to treatment. The isolation of TICs has been limited by the scarcity of this population in the tissue of origin and because the molecular signatures that characterize these cells are not well understood. Herein, we describe the generation of TIC-like cell lines by ectopic expression of the OCT4 transcription factor (TF) in primary breast cell preparations. Methods: OCT4 cDNA was over-expressed in four different primary human mammary epithelial (HMEC) breast cell preparations from reduction mammoplasty donors. OCT4-transduced breast cells (OTBCs) generated colonies (frequency similar to 0.01%) in self-renewal conditions (feeder cultures in human embryonic stem cell media). Differentiation assays, immunofluorescence, immunohistochemistry, and flow cytometry were performed to investigate the cell of origin of OTBCs. Serial dilutions of OTBCs were injected in nude mice to address their tumorigenic capabilities. gene expression microarrays were performed in OTBCs, and the role of downstream targets of OCT4 in maintaining self-renewal was investigated by knock-down experiments. Results: OTBCs overcame senescence, overexpressed telomerase, and down-regulated p16(INK4A). In differentiation conditions, OTBCs generated populations of both myoepithelial and luminal cells at low frequency, suggesting that the cell of origin of some OTBCs was a bi-potent stem cell. Injection of OTBCs in nude mice generated poorly differentiated breast carcinomas with colonization capabilities. gene expression microarrays of OTBC lines revealed a gene signature that was over-represented in the claudin-low molecular subtype of breast cancer. Lastly, siRNA-mediated knockdown of OCT4 or downstream embryonic targets of OCT4, such as NANOG and ZIC1, suppressed the ability of OTBCs to self-renew. Conclusions: Transduction of OCT4 in normal breast preparations led to the

关键词： Mesenchymal Marker gene expression microarray analysis Transcription Factor Network Early Progenitor Cell Mammary Epithelial Basal Medium

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A comprehensive assessment of methods for de-novo reverse-engineering of genome-scale regulatory networks

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GENOMICS 2011年第1期97卷 7-18页

作者： Narendra, Varun Lytkin, Nikita I. Aliferis, Constantin F. Statnikov, Alexander NYU Langone Med Ctr Ctr Hlth Informat & Bioinformat Sch Med New York NY 10016 USA NYU Sch Med Dept Pathol New York NY 10016 USA Vanderbilt Univ Dept Biostat Nashville TN 37232 USA NYU Sch Med Dept Med New York NY 10016 USA

De-novo reverse-engineering of genome-scale regulatory networks is an increasingly important objective for biological and translational research. While many methods have been recently developed for this task, their absolute and relative performance remains poorly understood. The present study conducts a rigorous performance assessment of 32 computational methods/variants for de-novo reverse-engineering of genome-scale regulatory networks by benchmarking these methods in 15 high-quality datasets and gold-standards of experimentally verified mechanistic knowledge. The results of this study show that some methods need to be substantially improved upon, while others should be used routinely. Our results also demonstrate that several univariate methods provide a "gatekeeper" performance threshold that should be applied when method developers assess the performance of their novel multivariate algorithms. Finally, the results of this study can be used to show practical utility and to establish guidelines for everyday use of reverse-engineering algorithms, aiming towards creation of automated data-analysis protocols and software systems. (C) 2010 Elsevier Inc. All rights reserved.

关键词： Regulatory network de-novo reverse-engineering Computational methods Evaluation gene expression microarray analysis

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A pathway-based approach to find novel markers of local glucocorticoid treatment in intermittent allergic rhinitis

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ALLERGY 2011年第1期66卷 132-140页

作者： Wang, H. Chavali, S. Mobini, R. Muraro, A. Barbon, F. Boldrin, D. Aberg, N. Benson, M. Univ Gothenburg Unit Clin Syst Biol S-40530 Gothenburg Sweden Univ Padua Dept Pediat Ctr Food Allergy Diag & Treatment I-35100 Padua Italy Univ Padua Dept Oncol & Surg Sci Padua Italy Queen Silvia Childrens Hosp Pediat Allergy Unit Gothenburg Sweden

P>Background: Glucocorticoids (GCs) may affect the expression of hundreds of genes in different cells and tissues from patients with intermittent allergic rhinitis (IAR). It is a formidable challenge to understand these complex changes by studying individual genes. In this study, we aimed to identify (i) pathways affected by local GC treatment and (ii) examine if those pathways could be used to find novel markers of local GC treatment in nasal fluids from patients with IAR. Methods: gene expression microarray- and iTRAQ-based proteomic analyses of nasal fluids, nasal fluid cells and nasal mucosa from patients with IAR were performed to find pathways enriched for differentially expressed genes and proteins. Proteins representing those pathways were analyzed with ELISA in an independent material of nasal fluids from 23 patients with IAR before and after treatment with a local GC. Results: Transcriptomal and proteomic high-throughput analyses of nasal fluids, nasal fluid cells and nasal mucosal showed that local GC treatment affected a wide variety of pathways in IAR such as the glucocorticoid receptor pathway and the acute phase response pathway. Extracellular proteins encoded by genes in those pathways were analyzed in an independent material of nasal fluids from patients. Proteins that changed significantly in expression included known biomarkers such as eosinophil cationic protein but also proteins that had not been previously described in IAR, namely CCL2, M-CSF, CXCL6 and apoH. Conclusion: Pathway-based analyses of genomic and proteomic high-throughput data can be used as a complementary approach to identify novel potential markers of GC treatment in IAR.

关键词： allergic rhinitis gene expression microarray analysis glucocorticoids proteomics

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miRNA regulation of cytotoxic effects in mouse Sertoli cells exposed to nonylphenol

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REPRODUCTIVE BIOLOGY AND ENDOCRINOLOGY 2011年第2011期9卷 126-126页

作者： Choi, Jin-Sung Oh, Jung-Hwa Park, Han-Jin Choi, Mi-Sun Park, Se-Myo Kang, Seung-Jun Oh, Moon-Ju Kim, Seung Jun Hwang, Seung Yong Yoon, Seokjoo Korea Inst Toxicol Div Res & Dev Taejon 305343 South Korea GenoCheck Co Ltd Ansan 426791 Gyeonggi Do South Korea Hanyang Univ Ansan 426791 Gyeonggi Do South Korea

Background: It is known that some environmental chemicals affect the human endocrine system. The harmful effects of endocrine disrupting chemical (EDC) nonylphenol (NP) have been studied since the 1980s. It is known that NP adversely affects physiological functions by mimicking the natural hormone 17 beta-estradiol. In the present study, we analyzed the expression of miRNAs and their target genes in mouse Sertoli TM4 cells to better understand the regulatory roles of miRNAs on Sertoli cells after NP exposure. Methods: Mouse TM4 Sertoli cells were treated with NP for 3 or 24 h, and global gene and miRNA expression were analyzed using Agilent mouse whole genome and mouse miRNA v13 arrays. Results: We identified genes that were > 2-fold differentially expressed in NP-treated cells and control cells (P < 0.05) and analyzed their functions through gene Ontology analysis. We also identified miRNAs that were differentially expressed in NP-treated and control cells. Of the 186 miRNAs the expression of which differed between NP-treated and control cells, 59 and 147 miRNAs exhibited 1.3-fold increased or decreased expression at 3 and 24 h, respectively. Network analysis of deregulated miRNAs suggested that Ppara may regulate the expression of certain miRNAs, including miR-378, miR-125a-3p miR-20a, miR-203, and miR-101a, after exposure to NP. Additionally, comprehensive analysis of predicted target genes for miRNAs showed that the expression of genes with roles in cell proliferation, the cell cycle, and cell death were regulated by miRNA in NP-treated TM4 cells. Levels of expression of the miRNAs miR-135a* and miR-199a-5p were validated by qRT-PCR. Finally, miR-135a* target gene analysis suggests that the generation of reactive oxygen species (ROS) following exposure to NP exposure may be mediated by miR-135a* through regulation of the Wnt/beta-catenin signaling pathway. Conclusions: Collectively, these data help to determine NP's actions on mouse TM4 Sertoli cells and increas

关键词： miRNA expression Sertoli Cell miRNA Target gene gene expression microarray analysis Induce Reactive Oxygen Species generation

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Multi-gene biomarker panel for reference free prostate cancer diagnosis: determination and independent validation

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BIOMARKERS 2010年第8期15卷 693-706页

作者： Cuperlovic-Culf, Miroslava Belacel, Nabil Davey, Michelle Ouellette, Rodney J. Natl Res Council Canada Inst Informat Technol Moncton NB E1A 7R1 Canada Atlantic Canc Res Inst Moncton NB Canada Dr Georges Dumont Hosp Moncton NB Canada

Identification of biomarkers that can accurately and reliably diagnose prostate cancer is clinically highly desirable. A novel classification method, K-closest resemblance was applied to several high-quality transcriptomic datasets of prostate cancer leading to the discovery of a panel of eight gene biomarkers that can detect prostate cancer with over 96% specificity and sensitivity in leave-one-out cross-validation. Independent validation on clinical samples confirmed the discriminatory power of this gene panel, yielding over 95% accuracy of diagnosis based on receiver-operating characteristic curve analyses. Different levels of validation of the proposed biomarker panel have shown that it allows extremely accurate diagnosis of prostate cancer. Application of this panel can possibly add a fast and objective tool to the pathologist's arsenal following further clinical testing.

关键词： Prostate cancer molecular diagnostic gene expression microarray analysis data analysis biomarker discovery

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Novel approach to gene expression profiling in Sezary syndrome

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BRITISH JOURNAL OF DERMATOLOGY 2010年第5期163卷 1090-1094页

作者： Pomerantz, R. G. Mirvish, E. D. Erdos, G. Falo, L. D., Jr. Geskin, L. J. Univ Pittsburgh Sch Med Dept Dermatol Pittsburgh PA 15213 USA

Background microarray hybridization studies in Sezary syndrome (SS) have compared T lymphocytes from patients with cutaneous T-cell lymphoma with those of normal controls;a major limitation of this design is that significant inherent genetic variability of lymphocyte populations between individuals may produce differences in gene expression unrelated to disease state. Objective The objective of this study was to minimize the heterogeneity of information derived from whole-genome expression analysis and to identify specific genetic differences between highly purified malignant and nonmalignant (control) T cells from the same patient with SS. Methods Peripheral blood mononuclear cells were obtained from a patient with SS, stained with anti-T-cell receptor V beta (TCR-V beta) antibodies, and sorted by multi-parameter flow cytometry. Malignant cells expressed the dominant TCR-V beta;control T cells lacked the dominant TCR-V beta but were otherwise phenotypically identical (CD3+CD4+CD45RO+). These cell populations were compared using the Illumina Inc. Sentrix Human-6 expression BeadChip system. Results Transcriptome analysis using the J5 test, which was selected for data analysis based on an efficiency analysis of competing statistical methods, showed differential expression of 44 genes between the malignant and nonmalignant cell subsets. Promyelocytic leukaemia zinc finger protein (ZBTB16) was the most profoundly upregulated gene in the malignant cell population, while interferon regulatory factor 3 (IRF3) and interferon-induced protein 35 (IFI35), which are important elements of the cellular response to viral infection, were significantly downregulated. Conclusions The results of this study suggest the feasibility of this novel comparative approach to genomic profiling in SS. Using this method, we identified several differentially expressed genes and pathways not previously described in SS. While these findings require validation in larger studies, they may be importan

关键词： cutaneous T-cell lymphoma gene expression microarray analysis genomics Sezary syndrome T-cell receptor beta-chain

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Insights in to the pathogenesis of axial spondyloarthropathy based on gene expression profiles

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ARTHRITIS RESEARCH & THERAPY 2009年第6期11卷 R168-R168页

作者： Sharma, Srilakshmi M. Choi, Dongseok Planck, Stephen R. Harrington, Christina A. Austin, Carrie R. Lewis, Jinnell A. Diebel, Tessa N. Martin, Tammy M. Smith, Justine R. Rosenbaum, James T. Oregon Hlth & Sci Univ Casey Eye Inst Portland OR 97239 USA Oregon Hlth & Sci Univ Dept Publ Hlth & Prevent Med Portland OR 97239 USA Oregon Hlth & Sci Univ Dept Cell & Dev Biol Portland OR 97239 USA Oregon Hlth & Sci Univ Dept Med Portland OR 97239 USA Oregon Hlth & Sci Univ Portland OR 97239 USA Oregon Hlth & Sci Univ Dept Mol Microbiol & Immunol Portland OR 97239 USA

Introduction Axial spondyloarthropathy (SpA) is a group of inflammatory diseases, with ankylosing spondylitis as the prototype. SpA affects the axial skeleton, entheses, joints and, at times, the eyes. This study tested the hypothesis that SpA is characterized by a distinct pattern of gene expression in peripheral blood of affected individuals compared with healthy controls. Methods High-density, human geneChip (R) probe arrays were used to profile mRNA of peripheral blood cells from 18 subjects with SpA and 25 normal individuals. Samples were processed as two separate sets at different times (11 SpA + 12 control subjects in primary set (Set 1);7 SpA+ 13 control subjects in the validation set (Set 2)). Blood samples were taken at a time when patients were not receiving systemic immunomodulatory therapy. Differential expression was defined as a 1.5-fold change with a q value < 5%. gene ontology and pathway information were also studied. Results Signals from 134 probe sets (representing 95 known and 12 unknown gene transcripts) were consistently different from controls in both Sets 1 and 2. Included among these were transcripts for a group of 20 genes, such as interleukin-1 (IL-1) receptors 1 and 2, Nod-like receptor family, pyrin domain containing 2 (NLRP2), secretory leukocyte peptidase inhibitor (SLPI), secreted protein acidic and rich in cysteine (SPARC), and triggering receptor expressed on myeloid cells 1 (TREM-1) that are clearly related to the immune or inflammatory response and a group of 4 transcripts that have a strong role in bone remodeling. Conclusions Our observations are the first to implicate SPARC, SLPI, and NLRP2, a component of the innate immune system, in the pathogenesis of SpA. Our results also indicate a possible role for IL-1 and its receptors in SpA. In accord with the bone pathology component of SpA, we also found that expression levels of transcripts reflecting bone remodeling factors are also distinguishable in peripheral blood from patien

关键词： Additional Data File Secretory Leukocyte Peptidase Inhibitor gene expression microarray analysis Endogenous Bone Morphogenetic Protein Systemic Immunomodulatory Therapy

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analysis of differential gene expression in colorectal cancer and stroma using fluorescence-activated cell sorting purification

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BRITISH JOURNAL OF CANCER 2009年第9期100卷 1452-1464页

作者： Smith, M. J. Culhane, A. C. Donovan, M. Coffey, J. C. Barry, B. D. Kelly, M. A. Higgins, D. G. Wang, J. H. Kirwan, W. O. Cotter, T. G. Redmond, H. P. Natl Univ Ireland Univ Coll Cork Acad Dept Surg Cork Ireland Natl Univ Ireland Univ Coll Cork Dept Biochem Cork Ireland Dana Farber Canc Inst Dept Biostat & Computat Biol Boston MA 02115 USA Harvard Univ Sch Publ Hlth Dept Biostat Boston MA 02115 USA Univ Coll Dublin Conway Inst Dublin 2 Ireland

Tumour stroma gene expression in biopsy specimens may obscure the expression of tumour parenchyma, hampering the predictive power of microarrays. We aimed to assess the utility of fluorescence-activated cell sorting (FACS) for generating cell populations for gene expression analysis and to compare the gene expression of FACS-purified tumour parenchyma to that of whole tumour biopsies. Single cell suspensions were generated from colorectal tumour biopsies and tumour parenchyma was separated using FACS. Fluorescence-activated cell sorting allowed reliable estimation and purification of cell populations, generating parenchymal purity above 90%. RNA from FACS-purified and corresponding whole tumour biopsies was hybridised to Affymetrix oligonucleotide microarrays. Whole tumour and parenchymal samples demonstrated differential gene expression, with 289 genes significantly overexpressed in the whole tumour, many of which were consistent with stromal gene expression (e. g., COL6A3, COL1A2, POSTN, TIMP2). genes characteristic of colorectal carcinoma were overexpressed in the FACS- purified cells (e. g., HOX2D and RHOB). We found FACS to be a robust method for generating samples for gene expression analysis, allowing simultaneous assessment of parenchymal and stromal compartments. Gross stromal contamination may affect the interpretation of cancer gene expression microarray experiments, with implications for hypotheses generation and the stability of expression signatures used for predicting clinical outcomes.

关键词： colorectal cancer fluorescence-activated cell sorting gene expression microarray analysis humans

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