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Related Concept Videos

Fast Reactions01:27

Fast Reactions

Fast reactions occurring in times shorter than the time needed to mix reactants pose a unique challenge for investigation. In a liquid-phase continuous-flow system, reactants A and B are swiftly pushed into the mixing chamber, where mixing occurs within 1 ms. The reaction mixture then flows through an observation tube, and one measures light absorption to determine species concentrations at various points of the tube. This method is most appropriate when relatively large volumes of reactants...
Reaction Mechanisms: Rate-limiting Step Approximation01:29

Reaction Mechanisms: Rate-limiting Step Approximation

The rate-determining step, or RDS, in a chemical reaction is the slowest step that determines the overall reaction rate. It is identified by using the observed rate law and typically involves approximation methods like the RDS approximation or the steady-state approximation.In the RDS approximation, also known as the rate-limiting-step or equilibrium approximation, the reaction mechanism consists of one or more reversible reactions near equilibrium, followed by a slower RDS, and then one or...
Response Surface Methodology01:16

Response Surface Methodology

Response Surface Methodology (RSM) is a collection of statistical and mathematical techniques used to develop, improve, and optimize processes. It is particularly valuable when many input variables or factors potentially influence a response variable.
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RACE - Rapid Amplification of cDNA Ends02:35

RACE - Rapid Amplification of cDNA Ends

Rapid Amplification of cDNA Ends, or RACE, is one of the most effective methods to obtain a full-length cDNA from an mRNA sequence between a known internal region to the unknown sequence at the 5’ or 3’ end. The unknown region is cloned in the cDNA by a gene-specific primer that binds the known end, and a hybrid primer that attaches a predefined anchor sequence to the unknown end of the cDNA. The sequence in between is amplified by PCR with an anchor primer and a gene-specific primer.
Since the...
Measuring Reaction Rates03:09

Measuring Reaction Rates

Polarimetry finds application in chemical kinetics to measure the concentration and reaction kinetics of optically active substances during a chemical reaction. Optically active substances have the capability of rotating the plane of polarization of linearly polarized light passing through them—a feature called optical rotation. Optical activity is attributed to the molecular structure of substances. Normal monochromatic light is unpolarized and possesses oscillations of the electrical field in...
RNA-seq03:21

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
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High-Throughput Metabolic Profiling for Model Refinements of Microalgae
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RSEA: A Web Server for Pathway Enrichment Analysis of Metabolic Reaction Sets.

Merve Yarıcı1, Furkan Cantürk2, Serdar Dursun3

  • 1Department of Bioengineering, Istanbul Medeniyet University, Istanbul, Turkey.

Biotechnology and Bioengineering
|May 9, 2025
PubMed
Summary

This study introduces Reaction Set Enrichment Analysis (RSEA), a web tool to analyze metabolic pathways. RSEA helps researchers interpret reaction sets from genome-scale metabolic models (GEMs) for better biological insights.

Keywords:
GPR rulesGenome‐Scale metabolic modelsfunctional enrichmentmetabolic pathways

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Area of Science:

  • Systems Biology
  • Metabolic Engineering
  • Computational Biology

Background:

  • Biological pathways are crucial for understanding metabolism.
  • Genome-scale metabolic models (GEMs) computationally represent organismal metabolism using reactions and gene-protein associations.
  • Analyzing reaction sets from GEMs for functional enrichment is challenging.

Purpose of the Study:

  • To introduce Reaction Set Enrichment Analysis (RSEA), a user-friendly web server tool.
  • To enable annotation of reaction sets to significantly related metabolic pathways.
  • To facilitate interpretation of metabolic changes predicted by GEMs.

Main Methods:

  • RSEA converts reaction lists derived from GEMs into standardized reaction identifiers.
  • The tool performs statistical enrichment analysis of reaction sets within metabolic pathways.
  • It provides a platform for exploring and interpreting reaction data.

Main Results:

  • RSEA offers a straightforward method for functional enrichment analysis of reaction sets.
  • The tool enhances the interpretation of metabolic flux predictions from GEMs.
  • It addresses the complexity of pathway analysis in systems biology.

Conclusions:

  • RSEA provides a practical solution for researchers analyzing metabolic pathways.
  • The web server facilitates the exploration and interpretation of reaction sets.
  • RSEA is freely available online to support metabolic research.