ArticleBMC bioinformatics2009
QPCR: Application for real-time PCR data management and analysis.
Article in BMC bioinformatics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
35 citing papers in PubMed, 67 citations in OpenAlex.
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- Ultra-Sensitive and Rapid Detection of PathogenicFoods (Basel, Switzerland) · 2022Article
- Auto-qPCR; a python-based web app for automated and reproducible analysis of qPCR data.Scientific reports · 2021Article
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- "Do my qPCR calculation", a web tool.Bioinformation · 2019Article
- CSF microRNA Profiling in Alzheimer's Disease: a Screening and Validation Study.Molecular neurobiology · 2017Article
- Tryptophan 2,3-dioxygenase and indoleamine 2,3-dioxygenase 1 make separate, tissue-specific contributions to basal and inflammation-induced kynurenine pathway metabolism in mice.Biochimica et biophysica acta · 2016Article
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- N-acetylaspartate catabolism determines cytosolic acetyl-CoA levels and histone acetylation in brown adipocytes.Scientific reports · 2016Article
- Mesoderm-specific transcript (MEST) is a negative regulator of human adipocyte differentiation.International journal of obesity (2005) · 2015Article
- Gene expression profiling of pre-eclamptic placentae by RNA sequencing.Scientific reports · 2015Article
- Regulation of aryl hydrocarbon receptor interacting protein (AIP) protein expression by MiR-34a in sporadic somatotropinomas.PloS one · 2015Article
- ERK1/2 and HIF1α Are Involved in Antiangiogenic Effect of Polyphenols-Enriched Fraction from Chilean Propolis.Evidence-based complementary and alternative medicine : eCAM · 2015Article
- Oligomerization, membrane association, and in vivo phosphorylation of sugarcane UDP-glucose pyrophosphorylase.The Journal of biological chemistry · 2014Article
- Molecular aspects of adipoepithelial transdifferentiation in mouse mammary gland.Stem cells (Dayton, Ohio) · 2014Article
- A survey of tools for the analysis of quantitative PCR (qPCR) data.Biomolecular detection and quantification · 2014Review
- Effects of oxidized phospholipids on gene expression in RAW 264.7 macrophages: a microarray study.PloS one · 2014Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundSince its introduction quantitative real-time polymerase chain reaction (qPCR) has become the standard method for quantification of gene expression. Its high sensitivity, large dynamic range, and accuracy led to the development of numerous applications with an increasing number of samples to be analyzed. Data analysis consists of a number of steps, which have to be carried out in several different applications. Currently, no single tool is available which incorporates storage, management, and multiple methods covering the complete analysis pipeline.
resultsQPCR is a versatile web-based Java application that allows to store, manage, and analyze data from relative quantification qPCR experiments. It comprises a parser to import generated data from qPCR instruments and includes a variety of analysis methods to calculate cycle-threshold and amplification efficiency values. The analysis pipeline includes technical and biological replicate handling, incorporation of sample or gene specific efficiency, normalization using single or multiple reference genes, inter-run calibration, and fold change calculation. Moreover, the application supports assessment of error propagation throughout all analysis steps and allows conducting statistical tests on biological replicates. Results can be visualized in customizable charts and exported for further investigation.
conclusionWe have developed a web-based system designed to enhance and facilitate the analysis of qPCR experiments. It covers the complete analysis workflow combining parsing, analysis, and generation of charts into one single application. The system is freely available at http://genome.tugraz.at/QPCR.
Indexed as
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.