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In a typical gene expression profiling experiment with multiple conditions, a common reference sample is used for co-hybridization with the samples to yield expression ratios. Differential expression for any other sample pair can then be calculated by assembling the ratios from their hybridizations with the reference. In this study we test the validity of this approach. Differential expression of a sample pair (i, j) was obtained in two ways: directly, by hybridizations of sample i versus j, and indirectly, by multiplying the expression ratios for hybridizations of sample i versus pool and pool versus sample j. We performed gene expression profiling using amphibian embryos (Xenopus laevis). Every sample combination of four different stages and a pool was profiled. Direct and indirect values were compared and used as the quality criterion for the data. Based on this criterion, 82% of all ratios were found to be sufficiently accurate. To increase the reliability of the signals, several widely used filtering techniques were tested. Filtering by differences of repeated hybridizations was found to be the optimal filter. Finally, we compared microarray-based gene expression profiles with the corresponding expression patterns obtained by whole-mount in situ hybridizations, resulting in a 90% correspondence.
Alizadeh,
Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling.
2000, Pubmed
Alizadeh,
Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling.
2000,
Pubmed Beissbarth,
Processing and quality control of DNA array hybridization data.
2000,
Pubmed Chomczynski,
Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction.
1987,
Pubmed DeRisi,
Exploring the metabolic and genetic control of gene expression on a genomic scale.
1997,
Pubmed Diehl,
Manufacturing DNA microarrays of high spot homogeneity and reduced background signal.
2001,
Pubmed Fellenberg,
Correspondence analysis applied to microarray data.
2001,
Pubmed Gasch,
Genomic expression programs in the response of yeast cells to environmental changes.
2000,
Pubmed Gawantka,
Gene expression screening in Xenopus identifies molecular pathways, predicts gene function and provides a global view of embryonic patterning.
1998,
Pubmed
,
Xenbase Gawantka,
Antagonizing the Spemann organizer: role of the homeobox gene Xvent-1.
1995,
Pubmed
,
Xenbase Glinka,
Combinatorial signalling by Xwnt-11 and Xnr3 in the organizer epithelium.
1996,
Pubmed
,
Xenbase Hinkley,
Sequential expression of multiple POU proteins during amphibian early development.
1992,
Pubmed
,
Xenbase Huber,
Variance stabilization applied to microarray data calibration and to the quantification of differential expression.
2002,
Pubmed Jenssen,
Analysis of repeatability in spotted cDNA microarrays.
2002,
Pubmed Johnson,
A Xenopus laevis gene encoding EF-1 alpha S, the somatic form of elongation factor 1 alpha: sequence, structure, and identification of regulatory elements required for embryonic transcription.
1995,
Pubmed
,
Xenbase Pollet,
Axeldb: a Xenopus laevis database focusing on gene expression.
2000,
Pubmed
,
Xenbase Raffelsberger,
Quality indicators increase the reliability of microarray data.
2002,
Pubmed Rajeevan,
Validation of array-based gene expression profiles by real-time (kinetic) RT-PCR.
2001,
Pubmed Shoemaker,
Recent developments in DNA microarrays.
2002,
Pubmed Smyth,
Statistical issues in cDNA microarray data analysis.
2003,
Pubmed Spellman,
Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization.
1998,
Pubmed Tibshirani,
Diagnosis of multiple cancer types by shrunken centroids of gene expression.
2002,
Pubmed Tran,
Microarray optimizations: increasing spot accuracy and automated identification of true microarray signals.
2002,
Pubmed
,
Xenbase Tusher,
Significance analysis of microarrays applied to the ionizing radiation response.
2001,
Pubmed VanBogelen,
Mapping regulatory networks in microbial cells.
1999,
Pubmed van 't Veer,
Gene expression profiling predicts clinical outcome of breast cancer.
2002,
Pubmed Wang,
Quantitative quality control in microarray image processing and data acquisition.
2001,
Pubmed Wittig,
Candidate genes for cross-resistance against DNA-damaging drugs.
2002,
Pubmed Yang,
Design issues for cDNA microarray experiments.
2002,
Pubmed Zien,
Centralization: a new method for the normalization of gene expression data.
2001,
Pubmed
