Independence and reproducibility across microarray platforms

Larkin, Jennie E.; Frank, Bryan; Gavras, Haralambos; Sultana, Răzvan; Quackenbush, John

doi:10.1038/nmeth757

Cited by 387 publications

(224 citation statements)

References 18 publications

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“…In insects, expression patterns of only a limited set of orthologs have been compared between the ant Camponotus festinantus and D. melanogaster (19). Guided by methodological conclusions of previous studies addressing the issue of gene expression comparisons between microarray platforms (20)(21)(22)(23)(24), we performed the first large-scale comparative analysis of insect development between A. gambiae and D. melanogaster. Our analysis shows a strong positive correlation of expression for 1,039 orthologous gene pairs and reveals that orthologs frequently share similar developmental expression patterns.…”

Section: Discussionmentioning

confidence: 99%

Life cycle transcriptome of the malaria mosquito Anopheles gambiae and comparison with the fruitfly Drosophila melanogaster

Koutsos

Blass

Meister

et al. 2007

Proc. Natl. Acad. Sci. U.S.A.

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The African mosquito Anopheles gambiae is the major vector of human malaria. We report a genome-wide survey of mosquito gene expression profiles clustered temporally into developmental programs and spatially into adult tissue-specific patterns. Global expression analysis shows that genes that belong to related functional categories or that encode the same or functionally linked protein domains are associated with characteristic developmental programs or tissue patterns. Comparative analysis of our data together with data published from Drosophila melanogaster reveal an overall strong and positive correlation of developmental expression between orthologous genes. The degree of correlation varies, depending on association of orthologs with certain developmental programs or functional groups. Interestingly, the similarity of gene expression is not correlated with the coding sequence similarity of orthologs, indicating that expression profiles and coding sequences evolve independently. In addition to providing a comprehensive view of temporal and spatial gene expression during the A. gambiae life cycle, this large-scale comparative transcriptomic analysis has detected important evolutionary features of insect transcriptomes.comparative transcriptomics ͉ insect development ͉ insect evolution ͉ microarrays A nopheles gambiae is the major vector of human malaria in subSaharan Africa, a secondary vector of filariasis, and the key vector of O'nyong-nyong viral fever outbreaks. Effective transmission of pathogens results from extreme anthropophilic behavior and repeated bloodfeeding of A. gambiae adult females. Indeed, female mosquitoes are found typically around human habitations and bloodfeed largely on humans rather than animals. Therefore, successful malaria control campaigns to date have coincided largely with local control of Anopheles populations.A substantial bloodmeal is required for A. gambiae egg development, the start of the next life cycle. Eggs are fertilized while traversing the genital chamber and begin embryonic development, which normally lasts 2-3 days and is similar to that of Drosophila melanogaster despite notable morphological (1) and molecular (2) differences. Four larval stages (instars) ensue, as compared with three in Drosophila, accompanied by continuous growth. In that period, larval organs are functional and adult organs incipient or slowly developing. During metamorphosis (from larva to pupa and adult) most larval organs are histolyzed, whereas others persist or grow.To date, molecular and cell biological research on A. gambiae has used D. melanogaster as the model system. These dipterans have diverged from a common ancestor Ϸ250 mya.

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Section: Discussionmentioning

confidence: 99%

Life cycle transcriptome of the malaria mosquito Anopheles gambiae and comparison with the fruitfly Drosophila melanogaster

Koutsos

Blass

Meister

et al. 2007

Proc. Natl. Acad. Sci. U.S.A.

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“…Because of the restricted availability of material suitable for gene expression analysis and with regard to the excellent correlation of mRNA gene expression data obtained by different microarray approaches with RQ-PCR data (Lossos et al, 2004;Larkin et al, 2005;Booken et al, 2008), we primarily aimed at a global gene expression analysis using Affymetrix TM U133A Gene Chips. These results were correlated with genomic profiles for the verification of gene dosage effects and candidate gene identification.…”

Section: Gene Expression Analysesmentioning

confidence: 99%

Microarray‐based genomic profiling reveals novel genomic aberrations in follicular lymphoma which associate with patient survival and gene expression status

Schwäenen

Viardot

Berger

et al. 2008

Genes Chromosomes & Cancer

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Follicular lymphoma (FL) is characterized by a large number of chromosomal aberrations. However, their exact genomic extension and involved target genes remain to be determined. For this purpose, we used array-based intermediate-high resolution genomic profiling in combination with Affymetrix TM gene expression analysis. Tumor specimens from 128 FL patients were analyzed for the presence of genomic aberrations and the results were correlated to clinical data sets and mRNA expression levels. In 114 (89%) of the 128 analyzed cases, a total of 688 genomic aberrations (384 gains/amplifications and 304 losses) were detected. Frequent genomic aberrations were: À1p36 (18%), þ2p15 (24%), À3q (14%), À6q (25%), þ7p (19%), þ7q (23%), þ8q (14%), À9p (16%), À11q (15%), þ12q (20%), À13q (11%), À17p (16%), þ18p (18%), and þ18q (28%). Critical segments of these imbalances were delineated to genomic fragments with a minimum size down to 0.2 Mb. By comparison of these with mRNA gene expression data, putative candidate genes were identified. Moreover, we found that deletions affecting the tumor suppressor gene CDKN2A/B on 9p21 were detected in nontransformed FL grade I-II. For this aberration as well as for À6q25 and À6q26, an association with inferior survival was observed.

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“…Even though, standardization is not yet progressed far enough to ensure an easy comparability of data from different sources, although it can be done in principle [118]. As a matter of fact, the quality and reproducibility of sample selection and preparation has become more problematic experimentally.…”

Section: Rna Analysismentioning

confidence: 99%

Microarray Technology as a Universal Tool for High-Throughput Analysis of Biological Systems

Sobek¹,

Bartscherer²,

Jacob³

et al. 2006

CCHTS

110

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Over the last years microarray technology has become one of the principal platform technologies for the highthroughput analysis of biological systems. Starting with the construction of first DNA microarrays in the 1990s, microarray technology has flourished in the last years and many different new formats have been developed. Peptide and protein microarrays are now applied for the elucidation of interaction partners, modification sites and enzyme substrates. Antibody microarrays are envisaged to be of high importance for the high-throughput determination of protein abundances in translational profiling approaches. First cell microarrays have been constructed to transform microarray technology from an in vitro technology to an in vivo functional analysis tool. All of these approaches share a common prerequisite: the solid support on which they are generated. The demands on this solid support are thereby as manifold as the applications themselves. This review is aimed to display the recent developments in surface chemistry and derivatization, and to summarize the latest developments in the different application areas of microarray technology.

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Independence and reproducibility across microarray platforms

Cited by 387 publications

References 18 publications

Life cycle transcriptome of the malaria mosquito Anopheles gambiae and comparison with the fruitfly Drosophila melanogaster

Life cycle transcriptome of the malaria mosquito Anopheles gambiae and comparison with the fruitfly Drosophila melanogaster

Microarray‐based genomic profiling reveals novel genomic aberrations in follicular lymphoma which associate with patient survival and gene expression status

Microarray Technology as a Universal Tool for High-Throughput Analysis of Biological Systems

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