Search Results
Search for other papers by Gilberto Paz-Filho in
Google Scholar
PubMed
Search for other papers by Claudio Alberto Mastronardi in
Google Scholar
PubMed
Search for other papers by Brian J Parker in
Google Scholar
PubMed
Search for other papers by Ainy Khan in
Google Scholar
PubMed
Search for other papers by Antonio Inserra in
Google Scholar
PubMed
Search for other papers by Klaus I Matthaei in
Google Scholar
PubMed
Search for other papers by Monika Ehrhart-Bornstein in
Google Scholar
PubMed
Search for other papers by Stefan Bornstein in
Google Scholar
PubMed
Search for other papers by Ma-Li Wong in
Google Scholar
PubMed
Search for other papers by Julio Licinio in
Google Scholar
PubMed
). Quality control of RNA and microarray samples The same amount of high-quality RNA from each of the samples was used for the transplanted and sham-operated groups. The assessment of RNA integrity on the Agilent Bioanalyzer 2100 indicated an average RNA
Search for other papers by Julian C Lui in
Google Scholar
PubMed
Program in Developmental Endocrinology and Genetics, Center for Molecular Medicine and Pediatric Endocrinology Unit, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, CRC, Room 1-3330, 10 Center Drive, MSC 1103, Bethesda, Maryland 20892-1103, USA
Search for other papers by Ola Nilsson in
Google Scholar
PubMed
Search for other papers by Jeffrey Baron in
Google Scholar
PubMed
necessarily involves studying one candidate gene at a time. However, recently, methods have been developed to study expression patterns of large numbers of genes in the growth plate, using microdissection, followed by microarray analysis ( Nilsson et al
Search for other papers by Petter Vikman in
Google Scholar
PubMed
Search for other papers by Joao Fadista in
Google Scholar
PubMed
Search for other papers by Nikolay Oskolkov in
Google Scholar
PubMed
using hybridization techniques such as northern blotting analysis ( Kevil et al . 1997 ) with the subsequent development allowing for the use of macroarrays ( Rast et al . 2000 ) and then microarrays ( Schena et al . 1995 ) and finally a fully
Search for other papers by R Sasik in
Google Scholar
PubMed
Search for other papers by CH Woelk in
Google Scholar
PubMed
Search for other papers by J Corbeil in
Google Scholar
PubMed
For many, analysis of a microarray experiment starts with a spreadsheet of expression levels. While great attention is duly paid to RNA extraction, preparation and hybridization, relatively little care is devoted to extraction of expression levels from the fluorescent image. By delegating this step to a click of the mouse the exact extraction process is masked and researchers may be unwittingly compromising their data. In this review, we describe the most common mistakes committed on the path from the image to the spreadsheet and their impact on data quality. Remedies are further proposed for most of the popular microarray platforms in use today.
Faculty of Medical and Human Sciences, Manchester Academic Health Science Centre, Paediatric and Adolescent Oncology, Stem Cell and Leukaemia Proteomics Laboratory, Musculoskeletal Research Group, Department Pediatrie, Faculty of Life Sciences, Institute of Human Development, University of Manchester, Manchester, UK
Search for other papers by A Stevens in
Google Scholar
PubMed
Faculty of Medical and Human Sciences, Manchester Academic Health Science Centre, Paediatric and Adolescent Oncology, Stem Cell and Leukaemia Proteomics Laboratory, Musculoskeletal Research Group, Department Pediatrie, Faculty of Life Sciences, Institute of Human Development, University of Manchester, Manchester, UK
Search for other papers by C De Leonibus in
Google Scholar
PubMed
Faculty of Medical and Human Sciences, Manchester Academic Health Science Centre, Paediatric and Adolescent Oncology, Stem Cell and Leukaemia Proteomics Laboratory, Musculoskeletal Research Group, Department Pediatrie, Faculty of Life Sciences, Institute of Human Development, University of Manchester, Manchester, UK
Search for other papers by D Hanson in
Google Scholar
PubMed
Faculty of Medical and Human Sciences, Manchester Academic Health Science Centre, Paediatric and Adolescent Oncology, Stem Cell and Leukaemia Proteomics Laboratory, Musculoskeletal Research Group, Department Pediatrie, Faculty of Life Sciences, Institute of Human Development, University of Manchester, Manchester, UK
Search for other papers by A W Dowsey in
Google Scholar
PubMed
Faculty of Medical and Human Sciences, Manchester Academic Health Science Centre, Paediatric and Adolescent Oncology, Stem Cell and Leukaemia Proteomics Laboratory, Musculoskeletal Research Group, Department Pediatrie, Faculty of Life Sciences, Institute of Human Development, University of Manchester, Manchester, UK
Search for other papers by A Whatmore in
Google Scholar
PubMed
Search for other papers by S Meyer in
Google Scholar
PubMed
Search for other papers by R P Donn in
Google Scholar
PubMed
Search for other papers by P Chatelain in
Google Scholar
PubMed
Faculty of Medical and Human Sciences, Manchester Academic Health Science Centre, Paediatric and Adolescent Oncology, Stem Cell and Leukaemia Proteomics Laboratory, Musculoskeletal Research Group, Department Pediatrie, Faculty of Life Sciences, Institute of Human Development, University of Manchester, Manchester, UK
Search for other papers by I Banerjee in
Google Scholar
PubMed
Search for other papers by K E Cosgrove in
Google Scholar
PubMed
Faculty of Medical and Human Sciences, Manchester Academic Health Science Centre, Paediatric and Adolescent Oncology, Stem Cell and Leukaemia Proteomics Laboratory, Musculoskeletal Research Group, Department Pediatrie, Faculty of Life Sciences, Institute of Human Development, University of Manchester, Manchester, UK
Search for other papers by P E Clayton in
Google Scholar
PubMed
Search for other papers by M J Dunne in
Google Scholar
PubMed
database of microarray experiments and gene expression profiles . Nucleic Acids Research 35 D747 – D750 . ( doi:10.1093/nar/gkl995 ). Patel L Clayton PE 2012 Predicting response to growth hormone treatment . Indian Journal of Pediatrics 79 229 – 237
Diabetes Research Center, Department of Clinical Chemistry and Radioimmunology, Department of Medical Biochemistry, Department of Biomedical Sciences, Brussels Free University (VUB), Laarbeeklaan 103, B1090 Brussel, Belgium
Search for other papers by G A Martens in
Google Scholar
PubMed
Search for other papers by E Motté in
Google Scholar
PubMed
Search for other papers by G Kramer in
Google Scholar
PubMed
Search for other papers by G Stangé in
Google Scholar
PubMed
Search for other papers by L W Gaarn in
Google Scholar
PubMed
Search for other papers by K Hellemans in
Google Scholar
PubMed
Search for other papers by J H Nielsen in
Google Scholar
PubMed
Search for other papers by J M Aerts in
Google Scholar
PubMed
Search for other papers by Z Ling in
Google Scholar
PubMed
Search for other papers by D Pipeleers in
Google Scholar
PubMed
) ( Fig. 3A ). Gene expression of 22 β cell markers was verified by real-time PCR. Only for Npy and St18 , the microarray and real-time PCR results were congruent. Relative to their Ppia (and Ubc , not shown) mRNA levels, neonatal β cells expressed
Search for other papers by Matthew L Rise in
Google Scholar
PubMed
Search for other papers by Susan E Douglas in
Google Scholar
PubMed
Search for other papers by Dionne Sakhrani in
Google Scholar
PubMed
Search for other papers by Jason Williams in
Google Scholar
PubMed
Search for other papers by K Vanya Ewart in
Google Scholar
PubMed
Search for other papers by Marlies Rise in
Google Scholar
PubMed
Search for other papers by William S Davidson in
Google Scholar
PubMed
Search for other papers by Ben F Koop in
Google Scholar
PubMed
Search for other papers by Robert H Devlin in
Google Scholar
PubMed
animals. Until recently, studies of the effects of GH on tissue gene expression have been hampered by the lack of genomic tools and methods for global gene expression profiling. The advent of DNA microarrays has allowed detailed analyses of the impacts of
Search for other papers by Angela Delaney in
Google Scholar
PubMed
Search for other papers by Vasantha Padmanabhan in
Google Scholar
PubMed
Search for other papers by Geoffrey Rezvani in
Google Scholar
PubMed
Search for other papers by Weiping Chen in
Google Scholar
PubMed
Search for other papers by Patricia Forcinito in
Google Scholar
PubMed
Search for other papers by Crystal S F Cheung in
Google Scholar
PubMed
Search for other papers by Jeffrey Baron in
Google Scholar
PubMed
Search for other papers by Julian C K Lui in
Google Scholar
PubMed
( Heinrichs et al . 1994 ). RNA integrity was confirmed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). Expression microarray No ovine-specific microarray was available commercially. However, sheep and cows differ at <3% of
Centre René Huguenin, FNCLCC, F-92210 St-Cloud, France INSERM, U735, F-92210 St-Cloud, France Functional Genomic Unit, Institut Gustave-Roussy, Villejuif, France ISPB, Faculté de Pharmacie de Lyon, Université Claude Bernard Lyon 1, Lyon F-69008, France Inserm, U590, Lyon F-69008, France Centre Léon Bérard, Lyon F-69008, France Département de Médecine, Centre René Huguenin, St-Cloud, France CNRS UMR 8125 Bioinformatics Unit, Institut Gustave-Roussy, Villejuif, France
Search for other papers by S Tozlu-Kara in
Google Scholar
PubMed
Search for other papers by V Roux in
Google Scholar
PubMed
Centre René Huguenin, FNCLCC, F-92210 St-Cloud, France INSERM, U735, F-92210 St-Cloud, France Functional Genomic Unit, Institut Gustave-Roussy, Villejuif, France ISPB, Faculté de Pharmacie de Lyon, Université Claude Bernard Lyon 1, Lyon F-69008, France Inserm, U590, Lyon F-69008, France Centre Léon Bérard, Lyon F-69008, France Département de Médecine, Centre René Huguenin, St-Cloud, France CNRS UMR 8125 Bioinformatics Unit, Institut Gustave-Roussy, Villejuif, France
Search for other papers by C Andrieu in
Google Scholar
PubMed
Centre René Huguenin, FNCLCC, F-92210 St-Cloud, France INSERM, U735, F-92210 St-Cloud, France Functional Genomic Unit, Institut Gustave-Roussy, Villejuif, France ISPB, Faculté de Pharmacie de Lyon, Université Claude Bernard Lyon 1, Lyon F-69008, France Inserm, U590, Lyon F-69008, France Centre Léon Bérard, Lyon F-69008, France Département de Médecine, Centre René Huguenin, St-Cloud, France CNRS UMR 8125 Bioinformatics Unit, Institut Gustave-Roussy, Villejuif, France
Centre René Huguenin, FNCLCC, F-92210 St-Cloud, France INSERM, U735, F-92210 St-Cloud, France Functional Genomic Unit, Institut Gustave-Roussy, Villejuif, France ISPB, Faculté de Pharmacie de Lyon, Université Claude Bernard Lyon 1, Lyon F-69008, France Inserm, U590, Lyon F-69008, France Centre Léon Bérard, Lyon F-69008, France Département de Médecine, Centre René Huguenin, St-Cloud, France CNRS UMR 8125 Bioinformatics Unit, Institut Gustave-Roussy, Villejuif, France
Search for other papers by J Vendrell in
Google Scholar
PubMed
Centre René Huguenin, FNCLCC, F-92210 St-Cloud, France INSERM, U735, F-92210 St-Cloud, France Functional Genomic Unit, Institut Gustave-Roussy, Villejuif, France ISPB, Faculté de Pharmacie de Lyon, Université Claude Bernard Lyon 1, Lyon F-69008, France Inserm, U590, Lyon F-69008, France Centre Léon Bérard, Lyon F-69008, France Département de Médecine, Centre René Huguenin, St-Cloud, France CNRS UMR 8125 Bioinformatics Unit, Institut Gustave-Roussy, Villejuif, France
Search for other papers by S Vacher in
Google Scholar
PubMed
Search for other papers by V Lazar in
Google Scholar
PubMed
Centre René Huguenin, FNCLCC, F-92210 St-Cloud, France INSERM, U735, F-92210 St-Cloud, France Functional Genomic Unit, Institut Gustave-Roussy, Villejuif, France ISPB, Faculté de Pharmacie de Lyon, Université Claude Bernard Lyon 1, Lyon F-69008, France Inserm, U590, Lyon F-69008, France Centre Léon Bérard, Lyon F-69008, France Département de Médecine, Centre René Huguenin, St-Cloud, France CNRS UMR 8125 Bioinformatics Unit, Institut Gustave-Roussy, Villejuif, France
Search for other papers by F Spyratos in
Google Scholar
PubMed
Search for other papers by M Tubiana-Hulin in
Google Scholar
PubMed
Centre René Huguenin, FNCLCC, F-92210 St-Cloud, France INSERM, U735, F-92210 St-Cloud, France Functional Genomic Unit, Institut Gustave-Roussy, Villejuif, France ISPB, Faculté de Pharmacie de Lyon, Université Claude Bernard Lyon 1, Lyon F-69008, France Inserm, U590, Lyon F-69008, France Centre Léon Bérard, Lyon F-69008, France Département de Médecine, Centre René Huguenin, St-Cloud, France CNRS UMR 8125 Bioinformatics Unit, Institut Gustave-Roussy, Villejuif, France
Centre René Huguenin, FNCLCC, F-92210 St-Cloud, France INSERM, U735, F-92210 St-Cloud, France Functional Genomic Unit, Institut Gustave-Roussy, Villejuif, France ISPB, Faculté de Pharmacie de Lyon, Université Claude Bernard Lyon 1, Lyon F-69008, France Inserm, U590, Lyon F-69008, France Centre Léon Bérard, Lyon F-69008, France Département de Médecine, Centre René Huguenin, St-Cloud, France CNRS UMR 8125 Bioinformatics Unit, Institut Gustave-Roussy, Villejuif, France
Search for other papers by P Cohen in
Google Scholar
PubMed
Search for other papers by P Dessen in
Google Scholar
PubMed
Centre René Huguenin, FNCLCC, F-92210 St-Cloud, France INSERM, U735, F-92210 St-Cloud, France Functional Genomic Unit, Institut Gustave-Roussy, Villejuif, France ISPB, Faculté de Pharmacie de Lyon, Université Claude Bernard Lyon 1, Lyon F-69008, France Inserm, U590, Lyon F-69008, France Centre Léon Bérard, Lyon F-69008, France Département de Médecine, Centre René Huguenin, St-Cloud, France CNRS UMR 8125 Bioinformatics Unit, Institut Gustave-Roussy, Villejuif, France
Search for other papers by R Lidereau in
Google Scholar
PubMed
Centre René Huguenin, FNCLCC, F-92210 St-Cloud, France INSERM, U735, F-92210 St-Cloud, France Functional Genomic Unit, Institut Gustave-Roussy, Villejuif, France ISPB, Faculté de Pharmacie de Lyon, Université Claude Bernard Lyon 1, Lyon F-69008, France Inserm, U590, Lyon F-69008, France Centre Léon Bérard, Lyon F-69008, France Département de Médecine, Centre René Huguenin, St-Cloud, France CNRS UMR 8125 Bioinformatics Unit, Institut Gustave-Roussy, Villejuif, France
Search for other papers by I Bièche in
Google Scholar
PubMed
has provided new insights into the involvement of gene networks and regulatory pathways in various tumoral processes ( DeRisi et al. 1996 ). cDNA and oligonucleotide microarrays are used to test the expression pattern of thousands of genes at a time
Search for other papers by Fei Wu in
Google Scholar
PubMed
Search for other papers by Ivan Ivanov in
Google Scholar
PubMed
Search for other papers by Rui Xu in
Google Scholar
PubMed
Department of Biochemistry and Biophysics, Department of Veterinary Physiology and Pharmacology, Institute of Biosciences and Technology, Texas A&M University, College Station, Texas 77843, USA
Department of Biochemistry and Biophysics, Department of Veterinary Physiology and Pharmacology, Institute of Biosciences and Technology, Texas A&M University, College Station, Texas 77843, USA
Search for other papers by Stephen Safe in
Google Scholar
PubMed
, Lobenhofer et al . 2002 , Coser et al . 2003 , Cunliffe et al . 2003 , Frasor et al . 2003 , 2004 , Scafoglio et al . 2006 ) and, in some microarray studies, E 2 decreased expression of more genes than it induced. In this study, we investigated the