Multiple-laboratory comparison of microarray platforms

Irizarry, Rafael A.; Warren, Daniel; Spencer, Forrest; Kim, Irene F.; Biswal, Shyam; Frank, Bryan; Gabrielson, Edward; Garcia, Joe G.N.; Geoghegan, Joel; Germino, Gregory G.; Griffin, Constance A.; Hilmer, Sara C.; Hoffman, Eric P.; Jedlicka, Anne; Kawasaki, Ernest S.; Martínez-Murillo, Francisco; Morsberger, Laura; Lee, Hannah; Petersen, David; Quackenbush, John; Scott, Alan L.; Wilson, Michael A.; Yang, Yanqin; Ye, Shui Qing; Yu, Wayne

doi:10.1038/nmeth756

Cited by 798 publications

(610 citation statements)

References 15 publications

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“…2,27 However, some infectious agents may also induce Th1 proliferation through TNFRSF4 signals. 22,28 In the context of allergy, however, recall responses were shown to be dependent on TNFRSF4 signals in an animal model of asthma. 29 TNFRSF4 has therefore been suggested as a therapeutic candidate in allergic disease.…”

Section: Discussionmentioning

confidence: 99%

A network-based analysis of allergen-challenged CD4+ T cells from patients with allergic rhinitis

Benson

Carlsson²,

Guillot

et al. 2006

Genes Immun

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We performed a network-based analysis of DNA microarray data from allergen-challenged CD4 þ T cells from patients with seasonal allergic rhinitis. Differentially expressed genes were organized into a functionally annotated network using the Ingenuity Knowledge Database, which is based on manual review of more than 200 000 publications. The main function of this network is the regulation of lymphocyte apoptosis, a role associated with several genes of the tuber necrosis factor superfamily. The expression of TNFRSF4, one of the genes in this family, was found to be 48 times higher in allergen-challenged cells than in diluent-challenged cells. TNFRSF4 is known to inhibit apoptosis and to enhance Th2 proliferation. Examination of a different material of allergen-stimulated peripheral blood mononuclear cells showed a higher number of interleukin-4 þ type 2 CD4 þ T (Th2) cells in patients than in controls (Po0.01), as well as a higher number of non-apoptotic Th2 cells in patients (Po0.01). The number of Th2 cells expressing TNFRSF4, TNFSF7 and TNFRSF1B was also significantly higher in patients. Treatment with anti-TNFSF4 resulted in a significantly decreased number of Th2 cells (Po0.05). A logical inference from all this is that the proliferation of allergen-challenged Th2 cells is associated with a decreased apoptosis of Th2 cells and an increase in TNFRSF4 signalling.

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Section: Discussionmentioning

confidence: 99%

A network-based analysis of allergen-challenged CD4+ T cells from patients with allergic rhinitis

Benson

Carlsson²,

Guillot

et al. 2006

Genes Immun

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“…Because IDR analysis is sensitive to the quality of replicates (Li et al 2011), to provide a more systematic comparison we generated a CAT plot (Irizarry et al 2005), including the comparison of each sample (Fig. 6A).…”

Section: Cold Spring Harbor Laboratory Press On May 12 2018 -Publishmentioning

confidence: 99%

Accounting for GC-content bias reduces systematic errors and batch effects in ChIP-seq data

Teng

Irizarry

2017

Genome Res.

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The main application of ChIP-seq technology is the detection of genomic regions that bind to a protein of interest. A large part of functional genomics' public catalogs is based on ChIP-seq data. These catalogs rely on peak calling algorithms that infer protein-binding sites by detecting genomic regions associated with more mapped reads (coverage) than expected by chance, as a result of the experimental protocol's lack of perfect specificity. We find that GC-content bias accounts for substantial variability in the observed coverage for ChIP-seq experiments and that this variability leads to false-positive peak calls. More concerning is that the GC effect varies across experiments, with the effect strong enough to result in a substantial number of peaks called differently when different laboratories perform experiments on the same cell line. However, accounting for GC content bias in ChIP-seq is challenging because the binding sites of interest tend to be more common in high GC-content regions, which confounds real biological signals with unwanted variability. To account for this challenge, we introduce a statistical approach that accounts for GC effects on both nonspecific noise and signal induced by the binding site. The method can be used to account for this bias in binding quantification as well to improve existing peak calling algorithms. We use this approach to show a reduction in false-positive peaks as well as improved consistency across laboratories.

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“…Since the work up procedure was very similar, the observed differences were probably more due to the platform and to the different probes than to the processes involved in amplification and hybridization. 46 Accordingly, additional methods were used to confirm mRNA expression data. The lower variation of spotted glass slide array is most likely due to the much lower dynamic rang of the FIGURE 3 -Real-time PCR analysis of selected genes that were modulated in LT97 cells by AE treatment according to cDNA microarrays: Effects of AE on the expression levels of GSTP1, GSTT2, GSTA4, UGT1A1 and UGT2B7 mRNA are shown.…”

Section: Discussionmentioning

confidence: 99%

Apple polyphenols modulate expression of selected genes related to toxicological defence and stress response in human colon adenoma cells

Selvaraju

Miene

Habermann

et al. 2008

Intl Journal of Cancer

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Apples contain significant amounts of flavonoids that are potentially cancer risk reducing by acting antioxidative or antiproliferative and by favorably modulating gene expression. The purpose of this study was to investigate whether polyphenols from apples modulate expression of genes related to colon cancer prevention in preneoplastic cells derived from colon adenoma (LT97). For this, LT97 cells were treated with effective concentrations of apple extracts (AEs). RNA was isolated and used for synthesis and labeling of cDNA that was hybridized to cDNA-arrays. Gene expression studies were performed using a commercial cDNA-array from Superarray ® that contains a limited number of genes (96 genes) related to drug metabolism, and a custom-made cDNA microarray that contains a higher number of genes (300 genes, including some genes from Superarray) related to mechanisms of carcinogenesis or chemoprevention. Real-time PCR and enzyme activity assays were additionally performed to confirm selected array results. Treatment of cells with AE resulted in 30 and 46 genes expressed over cut-off values ( 1.5-or 0.7-fold) in Superarray and custom array, respectively. Of 87 genes spotted on both arrays, 4 genes (CYP3A7, CYP4F3, CHST7, GSTT2) were regulated with similar directional changes. Expression of selected phase II genes (GSTP1, GSTT2, GSTA4, UGT1A1, UGT2B7), regulated on either array, was confirmed by real-time PCR. The enzyme activities of glutathione S-transferases and UDP-glucuronosyltransferases were altered by treatment of LT97 cells with AE. The observed altered gene expression patterns in LT97 cells, resulting from AE treatment, points to a possible protection of the cells against some toxicological insults.

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Multiple-laboratory comparison of microarray platforms

Cited by 798 publications

References 15 publications

A network-based analysis of allergen-challenged CD4+ T cells from patients with allergic rhinitis

A network-based analysis of allergen-challenged CD4+ T cells from patients with allergic rhinitis

Accounting for GC-content bias reduces systematic errors and batch effects in ChIP-seq data

Apple polyphenols modulate expression of selected genes related to toxicological defence and stress response in human colon adenoma cells

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