Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Hormonal Regulation of the Menstrual Cycle01:22

Hormonal Regulation of the Menstrual Cycle

1.7K
The ovarian cycle regulates endometrial changes throughout a single menstrual cycle via the coordinated action of gonadotrophin-releasing hormone (GnRH) and gonadotrophins.
At puberty, GnRH begins a pulsatile release pattern, which triggers the anterior pituitary gland to secrete follicle-stimulating hormone (FSH) and luteinizing hormone (LH). The frequency and amplitude of GnRH pulses vary across the menstrual cycle, with faster pulses favoring LH release and slower pulses favoring FSH...
1.7K
Gene Regulation During Sporulation01:17

Gene Regulation During Sporulation

503
Sporulation is a complex developmental process that allows certain Gram-positive bacteria, such as Bacillus subtilis and Clostridium species, to survive extreme environmental conditions. This process is tightly regulated by a series of signaling cascades and transcriptional controls, ensuring the formation of a highly resistant endospore.Sporulation is triggered by unfavorable conditions, such as nutrient depletion, and is governed by a phosphorelay system. One of the sensor kinases, such as...
503
Circadian Rhythms and Gene Regulation02:19

Circadian Rhythms and Gene Regulation

4.6K
The biological clock is involved in many aspects of regulating complex physiology in all animals. It was in 1935 when German zoologists, Hans Kalmus and Erwin Bünning, discovered the existence of circadian rhythm in Drosophila melanogaster. However, the internal molecular mechanisms behind the circadian clock remained a mystery until 1984, when Jeffrey C. Hall, Michael Rosbash, and Michael W. Young discovered the expression of the Per gene oscillating over a 24-hour cycle. In subsequent...
4.6K
Constitutive and Regulated Gene Expression01:27

Constitutive and Regulated Gene Expression

1.2K
Gene expression in prokaryotes is governed by constitutive and regulated systems, allowing cells to balance the production of essential proteins with adaptive responses to environmental changes.Constitutive Gene ExpressionConstitutive, or housekeeping, genes are continuously expressed as they encode proteins vital for fundamental cellular processes. These include enzymes for glycolysis, ribosomal components for protein synthesis, and proteins involved in DNA replication. Their constant...
1.2K
Negative Regulator Molecules01:23

Negative Regulator Molecules

38.5K
Positive regulators allow a cell to advance through cell cycle checkpoints. Negative regulators have an equally important role as they terminate a cell’s progression through the cell cycle—or pause it—until the cell meets specific criteria.
38.5K
The Z-Scheme of Electron Transport in Photosynthesis01:34

The Z-Scheme of Electron Transport in Photosynthesis

13.7K
The light reactions of photosynthesis assume a linear flow of electrons from water to NADP+. During this process, light energy drives the splitting of water molecules to produce oxygen. However, oxidation of water molecules is a thermodynamically unfavorable reaction and requires a strong oxidizing agent. This is accomplished by the first product of light reactions: oxidized P680 (or P680+), the most powerful oxidizing agent known in biology. The oxidized P680 that acquires an electron from the...
13.7K

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

The role of miR-335-5p in the redifferentiation of BRAF p.V600E thyroid cancers.

Molecular oncology·2026
Same author

Network-based analysis and multi-omics approaches for biology and medicine.

Biotechnology reports (Amsterdam, Netherlands)·2026
Same author

Precision Medicine Through Network Language: Integrating Clinical Insight and Data Expertise.

Genes·2026
Same author

ASGR2 and CLEC12A as Prognostically Relevant C-Type Lectin Hubs in Glioblastoma.

International journal of molecular sciences·2026
Same author

Network analysis predicts pembrolizumab response in advanced NSCLC with PD-L1 < 50.

Cancer cell international·2026
Same author

Exploring differential gene correlations in <i>Arabidopsis thaliana</i> for sustainable space farming.

Biotechnology reports (Amsterdam, Netherlands)·2026

Related Experiment Video

Updated: Feb 4, 2026

Studying Cell Cycle-regulated Gene Expression by Two Complementary Cell Synchronization Protocols
12:02

Studying Cell Cycle-regulated Gene Expression by Two Complementary Cell Synchronization Protocols

Published on: June 6, 2017

28.5K

A feature-based integrated scoring scheme for cell cycle-regulated genes prioritization.

Lorenzo Farina1, Paola Paci2

  • 1Department of Computer, Control and Management Engineering "A. Ruberti", Sapienza University of Rome, Italy; Institute for Systems Analysis and Computer Science "A. Ruberti", National Research Council, Rome, Italy.

Journal of Theoretical Biology
|September 28, 2018
PubMed
Summary

Identifying cell cycle-regulated genes is challenging due to inconsistent results. We developed PERLA (PERiodicity, Regulation, and Lag-Autocorrelation), a new scoring method that significantly improves gene prioritization and consistency across datasets in budding yeast.

Keywords:
Budding yeastCell cycleGene expressionTime-series

More Related Videos

Analysis of Combinatorial miRNA Treatments to Regulate Cell Cycle and Angiogenesis
11:44

Analysis of Combinatorial miRNA Treatments to Regulate Cell Cycle and Angiogenesis

Published on: March 30, 2019

8.0K
Using Human Differentially Expressed Gene Lists to Perform Downstream Pathway Enrichment Analysis and Target Prioritization
03:08

Using Human Differentially Expressed Gene Lists to Perform Downstream Pathway Enrichment Analysis and Target Prioritization

Published on: October 3, 2025

990

Related Experiment Videos

Last Updated: Feb 4, 2026

Studying Cell Cycle-regulated Gene Expression by Two Complementary Cell Synchronization Protocols
12:02

Studying Cell Cycle-regulated Gene Expression by Two Complementary Cell Synchronization Protocols

Published on: June 6, 2017

28.5K
Analysis of Combinatorial miRNA Treatments to Regulate Cell Cycle and Angiogenesis
11:44

Analysis of Combinatorial miRNA Treatments to Regulate Cell Cycle and Angiogenesis

Published on: March 30, 2019

8.0K
Using Human Differentially Expressed Gene Lists to Perform Downstream Pathway Enrichment Analysis and Target Prioritization
03:08

Using Human Differentially Expressed Gene Lists to Perform Downstream Pathway Enrichment Analysis and Target Prioritization

Published on: October 3, 2025

990

Area of Science:

  • Molecular Biology
  • Computational Biology
  • Genomics

Background:

  • Prioritizing cell cycle-regulated genes from gene expression time-profiles presents a significant computational challenge.
  • Poor overlap among gene lists generated by different experimental protocols hinders reliable identification.

Purpose of the Study:

  • To develop a robust computational method for prioritizing cell cycle-regulated genes in budding yeast.
  • To improve the consistency and reliability of gene identification across diverse experimental datasets.

Main Methods:

  • Focus on the budding yeast mitotic cell cycle, leveraging 12 datasets from 6 independent groups using 4 synchronization methods.
  • Proposed a novel multi-feature scoring algorithm named PERLA (PERiodicity, Regulation, and Lag-Autocorrelation).
  • Integrated diverse features of cell cycle-regulated gene expression time-profiles into the PERLA score.

Main Results:

  • PERLA demonstrated increased performance across a wide range of benchmarks.
  • Achieved substantially improved overlap of top-ranking genes among different datasets.
  • Validated the effectiveness of the proposed gene prioritization algorithm.

Conclusions:

  • The PERLA algorithm effectively addresses the challenge of prioritizing cell cycle-regulated genes.
  • Increased consistency across datasets facilitates more reliable biological insights.
  • Budding yeast serves as a critical model for cancer research and drug development, enhanced by improved gene prioritization.