The limits of log-ratios

Sharov, Vasily; Kwong, Ka Yin; Frank, Bryan; Chen, Emily; Gaspard, Renee; Yu, Yan; Yang, Ivana V.; Quackenbush, John

doi:10.1186/1472-6750-4-3

Cited by 31 publications

(15 citation statements)

References 4 publications

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“…Fewer DE genes were identified in LumB and Normal-like tumors. Similar analysis of the METABRIC data failed to identify any DE genes in the LumB subtype, and relatively few in Normal-like tumors (Table 1 ), likely due to the small number of samples, and the lower dynamic range of microarray data as compared to RNA-Seq 31 . We therefore restricted our subsequent analyses to LumA tumors.…”

Section: Resultsmentioning

confidence: 85%

Invasive lobular and ductal breast carcinoma differ in immune response, protein translation efficiency and metabolism

Zhu

Levine

et al. 2018

Sci Rep

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Invasive lobular carcinoma (ILC) is the second most common histological subtype of breast cancer following invasive ductal carcinoma (IDC). ILC differs from IDC in a number of histological and clinical features, such as single strand growth, difficulty in detection, and frequent late recurrences. To understand the molecular pathways involved in the clinical characteristics of ILC, we compared the gene expression profiles of luminal A ILC and luminal A IDC using data from TCGA and utilized samples from METABRIC as a validation data set. Top pathways that were significantly enriched in ILC were related to immune response. ILC exhibited a higher activity of almost all types of immune cells based on cell type-specific signatures compared to IDC. Conversely, pathways that were less enriched in ILC were related to protein translation and metabolism, which we functionally validated in cell lines. The higher immune activity uncovered in our study highlights the currently unexplored potential of a response to immunotherapy in a subset of patients with ILC. Furthermore, the lower rates of protein translation and metabolism - known features of tumor dormancy - may play a role in the late recurrences of ILC and lower detection rate in mammography and PET scanning.

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Section: Resultsmentioning

confidence: 85%

Invasive lobular and ductal breast carcinoma differ in immune response, protein translation efficiency and metabolism

Zhu

Levine

et al. 2018

Sci Rep

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“…For the microarray platforms, the discrimination between the target ratios is optimal near the middle of their dynamic range, and the ratios are “compressed” at both the lower and upper extremes. This constraint upon log 2 ratios has been previously described [ 15 ]. The ratios converge towards unity at lower end due to background noise, which is additive, and contributes to both samples being compared.…”

Section: Resultsmentioning

confidence: 99%

Evaluation of the External RNA Controls Consortium (ERCC) reference material using a modified Latin square design

et al. 2016

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Background: Highly multiplexed assays for quantitation of RNA transcripts are being used in many areas of biology and medicine. Using data generated by these transcriptomic assays requires measurement assurance with appropriate controls. Methods to prototype and evaluate multiple RNA controls were developed as part of the External RNA Controls Consortium (ERCC) assessment process. These approaches included a modified Latin square design to provide a broad dynamic range of relative abundance with known differences between four complex pools of ERCC RNA transcripts spiked into a human liver total RNA background. Results: ERCC pools were analyzed on four different microarray platforms: Agilent 1-and 2-color, Illumina bead, and NIAID lab-made spotted microarrays; and two different second-generation sequencing platforms: the Life Technologies 5500xl and the Illumina HiSeq 2500. Individual ERCC controls were assessed for reproducible performance in signal response to concentration among the platforms. Most demonstrated linear behavior if they were not located near one of the extremes of the dynamic range. Performance issues with any individual ERCC transcript could be attributed to detection limitations, platform-specific target probe issues, or potential mixing errors. Collectively, these pools of spike-in RNA controls were evaluated for suitability as surrogates for endogenous transcripts to interrogate the performance of the RNA measurement process of each platform. The controls were useful for establishing the dynamic range of the assay, as well as delineating the useable region of that range where differential expression measurements, expressed as ratios, would be expected to be accurate. Conclusions: The modified Latin square design presented here uses a composite testing scheme for the evaluation of multiple performance characteristics: linear performance of individual controls, signal response within dynamic range pools of controls, and ratio detection between pairs of dynamic range pools. This compact design provides an economical sample format for the evaluation of multiple external RNA controls within a single experiment per platform. These results indicate that well-designed pools of RNA controls, spiked into samples, provide measurement assurance for endogenous gene expression studies.

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“…By contrast, DNA microarrays show reliable results only for medium expression levels and therefore have a much smaller dynamic range. Thus, RNA-seq provides much more informative data, requiring less biological material and lower costs, becoming this technique popular for measuring gene expression on a large scale (Sharov et al, 2004; Wang et al, 2009). …”

Section: Rna-seq: Advantages and Limitationsmentioning

confidence: 99%

RNA-seq as a powerful tool for penaeid shrimp genetic progress

2014

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The sequences of all different RNA transcripts present in a cell or tissue that are related to the gene expression and its functional control represent what it is called a transcriptome. The transcripts vary between cells, tissues, ontogenetic and environmental conditions, and the knowledge that can be gained through them is of a solid relevance for genetic applications in aquaculture. Some of the techniques used in transcriptome studies, such as microarrays, are being replaced for next-generation sequencing approaches. RNA-seq emerges as a new possibility for the transcriptome complexity analysis as well as for the candidate genes and polymorphisms identification of penaeid species. Thus, it may also help to understand the determination of complex traits mechanisms and genetic improvement of stocks. In this review, it is first introduced an overview of transcriptome analysis by RNA-seq, followed by a discussion of how this approach may be applied in genetic progress within penaeid stocks.

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The limits of log-ratios

Abstract: Background: DNA microarray assays typically compare two biological samples and present the results of those comparisons gene-by-gene as the logarithm base two of the ratio of the measured expression levels for the two samples.

Cited by 31 publications

References 4 publications

Invasive lobular and ductal breast carcinoma differ in immune response, protein translation efficiency and metabolism

Invasive lobular and ductal breast carcinoma differ in immune response, protein translation efficiency and metabolism

Evaluation of the External RNA Controls Consortium (ERCC) reference material using a modified Latin square design

RNA-seq as a powerful tool for penaeid shrimp genetic progress

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