19 research outputs found

    A probe-treatment-reference (PTR) model for the analysis of oligonucleotide expression microarrays-5

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    Ference" across all the probe-sets. It is computed from the residual assessment after the PTR method with the invariant-set normalization on the data set "Expt-3-4".<p><b>Copyright information:</b></p><p>Taken from "A probe-treatment-reference (PTR) model for the analysis of oligonucleotide expression microarrays"</p><p>http://www.biomedcentral.com/1471-2105/9/194</p><p>BMC Bioinformatics 2008;9():194-194.</p><p>Published online 14 Apr 2008</p><p>PMCID:PMC2375129.</p><p></p

    A probe-treatment-reference (PTR) model for the analysis of oligonucleotide expression microarrays-4

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    E invariant-set normalization. The first reference array, , has been perturbed by adding noise. It shows a quite different distribution than others.<p><b>Copyright information:</b></p><p>Taken from "A probe-treatment-reference (PTR) model for the analysis of oligonucleotide expression microarrays"</p><p>http://www.biomedcentral.com/1471-2105/9/194</p><p>BMC Bioinformatics 2008;9():194-194.</p><p>Published online 14 Apr 2008</p><p>PMCID:PMC2375129.</p><p></p

    A probe-treatment-reference (PTR) model for the analysis of oligonucleotide expression microarrays-0

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    Ing of summarization. Here, we only illustrate the cross strategy for the reference and target selection.<p><b>Copyright information:</b></p><p>Taken from "A probe-treatment-reference (PTR) model for the analysis of oligonucleotide expression microarrays"</p><p>http://www.biomedcentral.com/1471-2105/9/194</p><p>BMC Bioinformatics 2008;9():194-194.</p><p>Published online 14 Apr 2008</p><p>PMCID:PMC2375129.</p><p></p

    A probe-treatment-reference (PTR) model for the analysis of oligonucleotide expression microarrays-2

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    Ent of non-spike-in genes. The PTR method gives the smallest variation for all three normalization algorithms.<p><b>Copyright information:</b></p><p>Taken from "A probe-treatment-reference (PTR) model for the analysis of oligonucleotide expression microarrays"</p><p>http://www.biomedcentral.com/1471-2105/9/194</p><p>BMC Bioinformatics 2008;9():194-194.</p><p>Published online 14 Apr 2008</p><p>PMCID:PMC2375129.</p><p></p

    A probe-treatment-reference (PTR) model for the analysis of oligonucleotide expression microarrays-3

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    <p><b>Copyright information:</b></p><p>Taken from "A probe-treatment-reference (PTR) model for the analysis of oligonucleotide expression microarrays"</p><p>http://www.biomedcentral.com/1471-2105/9/194</p><p>BMC Bioinformatics 2008;9():194-194.</p><p>Published online 14 Apr 2008</p><p>PMCID:PMC2375129.</p><p></p

    A probe-treatment-reference (PTR) model for the analysis of oligonucleotide expression microarrays-1

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    1 and C1): the reference is the perturbed array ; Middle column: the reference in both A2 and C2 is , while the reference in B2 is the pseudo-reference defined as the average quantiles of all six arrays; Right column (A3, B3 and C3): the result obtained by the PTR method using all six arrays as references. The grey dots are non-spike-in genes; the black dots are spike-in genes which are expected to have log-ratio M = 1. We can see that the PTR method results are not affected by the perturbed array and offers the smallest variation for non-spike-in genes.<p><b>Copyright information:</b></p><p>Taken from "A probe-treatment-reference (PTR) model for the analysis of oligonucleotide expression microarrays"</p><p>http://www.biomedcentral.com/1471-2105/9/194</p><p>BMC Bioinformatics 2008;9():194-194.</p><p>Published online 14 Apr 2008</p><p>PMCID:PMC2375129.</p><p></p

    Inference of transcription modification in long-live yeast strains from their expression profiles-0

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    <p><b>Copyright information:</b></p><p>Taken from "Inference of transcription modification in long-live yeast strains from their expression profiles"</p><p>http://www.biomedcentral.com/1471-2164/8/219</p><p>BMC Genomics 2007;8():219-219.</p><p>Published online 6 Jul 2007</p><p>PMCID:PMC1949827.</p><p></p>t in three long-lived mutants. The x-axis is the threshold for up-regulation. The y-axis is the negative log transformed p-value. The red, green, and blue line correspond to Δ, Δ, and Δ mutant, respectively

    Validation of mature and precursor miRNA activation by the tagged RT-PCR assay.

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    (A) Schematic of the tagged semi-quantitative RT-PCR strategy used for precursor and mature miRNA amplification in monocytes treated with LPS or medium alone. (B) RT-PCR analysis reveals detection of the precursor and mature forms of LPS-upregulated miRNAs hsa-mir-155, hsa-mir-146a, hsa-mir-9, hsa-mir-147b, and hsa-mir-193a, as well as control hsa-mir-21 after 6 hours of culture (n = 3). Black triangles denote gel band size of precursor miRNAs, while black arrows denote the mature miRNAs. Mk = marker, L = LPS-treated, M = medium-only.</p

    Expression validation of mature miRNAs in LPS-treated monocytes by quantitative RT-PCR.

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    The abundance of signature miRNAs was quantified relative to U6 RNA and shown in black points for the LPS-treated monocytes or gray points for the medium-treated monocytes. Samples from nine healthy donors were tested for the 6-hour timepoint, and six healthy donors were tested for the 24-hour timepoint. Taqman-based qRT-PCR assays to detect mature miRNA expression confirmed statistically significant upregulation of hsa-mir-155 (A), hsa-mir-146a (B), hsa-mir-9 (C) and has-mir-147b (D) at both timepoints. qRT-PCR confirmed statistically significant upregulation of hsa-mir-187 (E), hsa-mir-193a (F), hsa-mir-99b (G), hsa-mir-125-5p, (H), and hsa-mir-125-3p (I) at 24 hours. MiRNA species (J) hsa-mir-2116 (K) hsa-mir-146b, (L) hsa-mir-449c, (M) hsa-mir-149, and (N) hsa-mir-365b were not differentially expressed at either timepoint. P-values were determined using the two-tailed Student’s paired t-test.</p
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