Location of Repository

Performance comparison of two microarray platforms to assess differential gene expression in human monocyte and macrophage cells

By Seraya Maouche, Odette Poirier, Tiphaine Godefroy, Robert Olaso, Ivo Gut, Jean-Phillipe Collet, Gilles Montalescot and François Cambien
Topics: Research Article
Publisher: BioMed Central
OAI identifier: oai:pubmedcentral.nih.gov:2464609
Provided by: PubMed Central
Download PDF:
Sorry, we are unable to provide the full text but you may find it at the following location(s):
  • http://www.pubmedcentral.nih.g... (external link)
  • Suggested articles

    Preview

    Citations

    1. (2000). Gene expression studies using microarrays: principles, problems, and prospects. Adv Physiol Educ
    2. (2007). Perspectives and limitations of microarray-based gene expression profiling of thyroid tumors. Endocr Rev
    3. (2006). Microarray data reproduced, but some concerns remain. Science
    4. (2006). The MicroArray Quality Control (MAQC) project shows interand intraplatform reproducibility of gene expression measurements. Nat Biotechnol
    5. (2006). et al.: Performance comparison of one-color and twocolor platforms within the MicroArray Quality Control (MAQC) project. Nat Biotechnol
    6. (2006). Rat toxicogenomic study reveals analytical consistency across microarray platforms. Nat Biotechnol
    7. (2006). et al.: Evaluation of DNA microarray results with quantitative gene expression platforms. Nat Biotechnol
    8. (2006). Using RNA sample titrations to assess microarray platform performance and normalization techniques. Nat Biotechnol
    9. (2006). et al.: Evaluation of external RNA controls for the assessment of microarray performance.
    10. (2007). Reproducible and reliable microarray results through quality control: good laboratory proficiency and appropriate data analysis practices are essential. Curr Opin Biotechnol
    11. (2007). Tsai CA: Reproducibility of microarray data: a further analysis of microarray quality control (MAQC) data.
    12. (2007). Reply to MAQC papers over the cracks. Nature Biotechnology
    13. The Gene Ontology (GO) project [http://www.geneontol ogy.org]
    14. (2006). The mononuclear phagocyte system. Curr Opin Immunol
    15. (2006). Inflammation and atherosclerosis. Annu Rev Pathol
    16. (1996). Expression monitoring by hybridization to high-density oligonucleotide arrays. Nat Biotechnol
    17. (2004). Decoding randomly ordered DNA arrays. Genome Res
    18. (2005). Experimental comparison and cross-validation of the Affymetrix and Illumina gene expression analysis platforms. Nucleic Acids Res
    19. (2006). An open-access long oligonucleotide microarray resource for analysis of the human and mouse transcriptomes. Nucleic Acids Res
    20. (2004). Functional plasticity of macrophages: reversible adaptation to changing microenvironments.
    21. (2007). cDNA microarray analysis reveals fundamental differences in the expression profiles of primary human monocytes, monocyte-derived macrophages, and alveolar macrophages.
    22. (2006). Rickman DS: Comparison of the latest commercial short and long oligonucleotide microarray technologies.
    23. (2007). Three methods for optimization of crosslaboratory and cross-platform microarray expression data. Nucleic Acids Res
    24. (2007). A rapid method for microarray cross platform comparisons using gene expression signatures. Mol Cell Probes
    25. (2007). CJ: Selection of differentially expressed genes in microarray data analysis.
    26. (2007). L: QA/QC issues to aid regulatory acceptance of microarray gene expression data. Environ Mol Mutagen
    27. (2007). Analyzing gene expression data in terms of gene sets: methodological issues. Bioinformatics
    28. (2005). Mesirov JP: Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles.
    29. (2006). A: Transcriptional profiling of the human monocyte-to-macrophage differentiation and polarization: new molecules and patterns of gene expression.
    30. (1996). A language for data analysis and graphics.
    31. (2006). Tavaré S: Quality control and low-level statistical analysis of Illumina BeadArrays. Revstat
    32. (2003). Speed TP: Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res
    33. (2004). Bioconductor: open software development for computational biology and bioinformatics. Genome Biol
    34. (2003). Speed TP: Normalization of cDNA microarray data. Methods
    35. (2003). NetAffx: Affymetrix probesets and annotations. Nucleic Acids Res
    36. (2007). Mediante: a web-based microarray data manager. Bioinformatics
    37. MAQC project annotation data [http://www.nature.com]
    38. Limma: linear models for microarray data.
    39. (1995). Controlling the false discovery rate: a practical and powerful approach to multiple testing.
    40. (2002). A direct approach to false discovery rates.
    41. (2005). Simple procedure for estimating the false discovery rate. Bioinformatics
    42. (2000). Cambpell MJ: Transcription, genomes, function. Trends in Genetics

    To submit an update or takedown request for this paper, please submit an Update/Correction/Removal Request.