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      Applications for Microarrays in Renal Biology and Medicine

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          Abstract

          Groundbreaking recent developments, such as the near completion of human and mouse genome sequencing efforts and the emergence of robust microarray (gene chip) technologies, enabling comprehensive analysis of transcriptomes, provide new opportunities of unprecedented scale for researchers of kidney biology and disease. Combined with advanced computational and mathematical approaches for microarray data analysis, microarray applications promise to revolutionize our understanding of molecular mechanisms of kidney development and renal pathogenesis. New knowledge in this field will facilitate new approaches for molecular diagnostics, drug discovery, and eventually ‘personalized’ renal medicine. In this review, we outline current and future research applications of microarray and computational approaches in renal biology and disease. We describe basic steps in microarray data analysis and introduce advanced computational approaches to optimize data mining of vast microarray datasets.

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          Most cited references 15

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          Molecular classification of cutaneous malignant melanoma by gene expression profiling.

          The most common human cancers are malignant neoplasms of the skin. Incidence of cutaneous melanoma is rising especially steeply, with minimal progress in non-surgical treatment of advanced disease. Despite significant effort to identify independent predictors of melanoma outcome, no accepted histopathological, molecular or immunohistochemical marker defines subsets of this neoplasm. Accordingly, though melanoma is thought to present with different 'taxonomic' forms, these are considered part of a continuous spectrum rather than discrete entities. Here we report the discovery of a subset of melanomas identified by mathematical analysis of gene expression in a series of samples. Remarkably, many genes underlying the classification of this subset are differentially regulated in invasive melanomas that form primitive tubular networks in vitro, a feature of some highly aggressive metastatic melanomas. Global transcript analysis can identify unrecognized subtypes of cutaneous melanoma and predict experimentally verifiable phenotypic characteristics that may be of importance to disease progression.
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            Computational analysis of microarray data.

            Microarray experiments are providing unprecedented quantities of genome-wide data on gene-expression patterns. Although this technique has been enthusiastically developed and applied in many biological contexts, the management and analysis of the millions of data points that result from these experiments has received less attention. Sophisticated computational tools are available, but the methods that are used to analyse the data can have a profound influence on the interpretation of the results. A basic understanding of these computational tools is therefore required for optimal experimental design and meaningful data analysis.
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              NPHS2, encoding the glomerular protein podocin, is mutated in autosomal recessive steroid-resistant nephrotic syndrome.

              Familial idiopathic nephrotic syndromes represent a heterogeneous group of kidney disorders, and include autosomal recessive steroid-resistant nephrotic syndrome, which is characterized by early childhood onset of proteinuria, rapid progression to end-stage renal disease and focal segmental glomerulosclerosis. A causative gene for this disease, NPHS2, was mapped to 1q25-31 and we report here its identification by positional cloning. NPHS2 is almost exclusively expressed in the podocytes of fetal and mature kidney glomeruli, and encodes a new integral membrane protein, podocin, belonging to the stomatin protein family. We found ten different NPHS2 mutations, comprising nonsense, frameshift and missense mutations, to segregate with the disease, demonstrating a crucial role for podocin in the function of the glomerular filtration barrier.
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                Author and article information

                Journal
                EXN
                Nephron Exp Nephrol
                10.1159/issn.1660-2129
                Cardiorenal Medicine
                S. Karger AG
                978-3-8055-7383-2
                978-3-318-00822-7
                1660-2129
                2002
                2002
                05 April 2002
                : 10
                : 2
                : 93-101
                Affiliations
                Division of Nephrology, Department of Medicine, Albert Einstein College of Medicine and Albert Einstein NIDDK Biotechnology Center, Bronx, N.Y., USA
                Article
                49904 Exp Nephrol 2002;10:93–101
                10.1159/000049904
                11937756
                © 2002 S. Karger AG, Basel

                Copyright: All rights reserved. No part of this publication may be translated into other languages, reproduced or utilized in any form or by any means, electronic or mechanical, including photocopying, recording, microcopying, or by any information storage and retrieval system, without permission in writing from the publisher. Drug Dosage: The authors and the publisher have exerted every effort to ensure that drug selection and dosage set forth in this text are in accord with current recommendations and practice at the time of publication. However, in view of ongoing research, changes in government regulations, and the constant flow of information relating to drug therapy and drug reactions, the reader is urged to check the package insert for each drug for any changes in indications and dosage and for added warnings and precautions. This is particularly important when the recommended agent is a new and/or infrequently employed drug. Disclaimer: The statements, opinions and data contained in this publication are solely those of the individual authors and contributors and not of the publishers and the editor(s). The appearance of advertisements or/and product references in the publication is not a warranty, endorsement, or approval of the products or services advertised or of their effectiveness, quality or safety. The publisher and the editor(s) disclaim responsibility for any injury to persons or property resulting from any ideas, methods, instructions or products referred to in the content or advertisements.

                Page count
                Figures: 1, Tables: 2, References: 36, Pages: 9
                Product
                Self URI (application/pdf): https://www.karger.com/Article/Pdf/49904
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