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Related Concept Videos

Real Time RT-PCR02:57

Real Time RT-PCR

Real-time reverse transcription-polymerase chain reaction, or Real-time RT-PCR, is an analytical tool used to determine the expression level of target genes. The method involves converting mRNA to complementary DNA with the help of an enzyme known as reverse transcriptase, followed by the PCR amplification of the cDNA. These two processes can be performed simultaneously in a single tube or separately as a two-step reaction.
The real-time quantification of the number of amplified products is...
Comparing Copy Number Variations and SNPs02:26

Comparing Copy Number Variations and SNPs

Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
DNA Microarrays02:34

DNA Microarrays

Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...

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Related Experiment Video

Updated: Jul 2, 2026

qPCRTag Analysis - A High Throughput, Real Time PCR Assay for Sc2.0 Genotyping
07:00

qPCRTag Analysis - A High Throughput, Real Time PCR Assay for Sc2.0 Genotyping

Published on: May 25, 2015

GeneQuantify: a web-based tool for qPCR gene expression and copy number variation analysis.

Burhanettin Yalçınkaya1

  • 1TUBITAK National Metrology Institute (TUBITAK UME), Gebze, Kocaeli, Turkey. burhanettin.yalcinkaya@tubitak.gov.tr.

Molecular and Cellular Biochemistry
|July 1, 2026
PubMed
Summary
This summary is machine-generated.

GeneQuantify is a new web platform simplifying quantitative PCR (qPCR) data analysis for gene expression and copy number variation studies. It offers automated calculations, quality control, and statistical testing, enhancing reproducibility in molecular research.

Keywords:
MIQEcopy number variationgeNormgene expressionqPCRrelative quantificationstatistical automationweb-based tool

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Area of Science:

  • Molecular Biology
  • Bioinformatics
  • Clinical Biochemistry

Background:

  • Quantitative polymerase chain reaction (qPCR) is crucial for gene expression and copy number variation (CNV) analysis in clinical settings.
  • Interpreting qPCR data requires advanced bioinformatics expertise for normalization, statistical testing, and visualization.
  • A need exists for user-friendly tools to streamline and standardize qPCR data evaluation.

Purpose of the Study:

  • To develop GeneQuantify, a web-based platform for user-friendly and standardized qPCR data analysis.
  • To integrate robust statistical frameworks and quality control modules into the platform.
  • To enhance reproducibility, transparency, and workflow efficiency in molecular research.

Main Methods:

  • Developed a web application using Python and Streamlit (GeneQuantify).
  • Integrated features for data input (manual, spreadsheet, RDML/RDES), automated calculations (ΔCq, ΔΔCq, relative expression), and normalization (geNorm).
  • Included automated outlier detection, amplification efficiency correction, statistical validity testing (Shapiro-Wilk, Levene's), and an automated statistical decision pipeline with FDR corrections.

Main Results:

  • GeneQuantify provides automated calculations, quality control, statistical decision-making, and visualization for qPCR data.
  • The platform supports multi-reference gene normalization and automated outlier detection.
  • Validated accuracy against manual calculations, showing consistent results across various scenarios.

Conclusions:

  • GeneQuantify offers an accessible, integrated environment for qPCR analysis, aligning with MIQE guidelines.
  • The platform enhances reproducibility, transparency, and workflow efficiency in molecular research, clinical biochemistry, and education.
  • Automated statistical selection and multi-language support improve international accessibility and usability.