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

Gene Conversion02:08

Gene Conversion

9.9K
Other than maintaining genome stability via DNA repair, homologous recombination plays an important role in diversifying the genome. In fact, the recombination of sequences forms the molecular basis of genomic evolution. Random and non-random permutations of genomic sequences create a library of new amalgamated sequences. These newly formed genomes can determine the fitness and survival of cells. In bacteria, homologous and non-homologous types of recombination lead to the evolution of new...
9.9K
Epistasis Analysis01:09

Epistasis Analysis

5.1K
Although Mendel chose seven unrelated traits in peas to study gene segregation, most traits involve multiple gene interactions that create a spectrum of phenotypes. When the interaction of various genes or alleles at different locations influences a phenotype, this is called epistasis. Epistasis often involves one gene masking or interfering with the expression of another (antagonistic epistasis). Epistasis often occurs when different genes are part of the same biochemical pathway. The...
5.1K
Genetic Screens02:46

Genetic Screens

5.0K
Genetic screens are tools used to identify genes and mutations responsible for phenotypes of interest. Genetic screens help identify individuals or a group of people at risk of developing  genetic diseases and help them with early intervention, targeted therapy, and reproductive options.
Forward genetic screens
Forward or “classical” genetic screens involve creating random mutations in an organism’s DNA using radiation, mutagens, or insertion of additional bases, which...
5.0K
Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

6.1K
Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
6.1K
Genetic Variation01:25

Genetic Variation

357
Genetic variation is the diversity in DNA sequences found among individuals of the same species. This diversity is crucial for a species' survival because it helps organisms adapt to environmental changes. Genetic variation begins with fertilization, where an egg and sperm cell merge. Each of these cells carries 23 chromosomes, up to 46 in the fertilized egg. Chromosomes are long DNA strands that contain genes, the basic units of heredity.
Genes exist in different versions called alleles,...
357
Gene Evolution - Fast or Slow?02:05

Gene Evolution - Fast or Slow?

7.3K
The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code...
7.3K

You might also read

Related Articles

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

Sort by
Same author

Reamed and unreamed intramedullary nailing for the treatment of open and closed tibial fractures: a subgroup analysis of randomised trials.

International orthopaedics·2009
Same author

Selective COX-2 inhibitor versus nonselective COX-1 and COX-2 inhibitor in the prevention of heterotopic ossification after total hip arthroplasty: a meta-analysis of randomised trials.

International orthopaedics·2009
Same author

[Study on evaluating sex determining region of the Y as an engrafting track of BMSCs transplantation for repairing osteonecrosis of the femoral head of rabbit].

Zhongguo xiu fu chong jian wai ke za zhi = Zhongguo xiufu chongjian waike zazhi = Chinese journal of reparative and reconstructive surgery·2009
Same author

Positive association between benign familial infantile convulsions and LGI4.

Brain & development·2009
Same author

Catalytic enantioselective synthesis of chiral phthalides by efficient reductive cyclization of 2-acylarylcarboxylates under aqueous transfer hydrogenation conditions.

Organic letters·2009
Same author

Significance of urinary liver-fatty acid-binding protein in cardiac catheterization in patients with coronary artery disease.

Internal medicine (Tokyo, Japan)·2009

Related Experiment Video

Updated: Aug 23, 2025

An Allele-specific Gene Expression Assay to Test the Functional Basis of Genetic Associations
10:17

An Allele-specific Gene Expression Assay to Test the Functional Basis of Genetic Associations

Published on: November 3, 2010

23.0K

Assessing equivalent and inverse change in genes between diverse experiments.

Lisa Neums1,2, Devin C Koestler1,2, Qing Xia1,2

  • 1Department of Biostatistics and Data Science, University of Kansas Medical Center, Kansas City, KS, United States.

Frontiers in Bioinformatics
|October 28, 2022
PubMed
Summary

A new bootstrap test for the Equivalent Change Index (ECI) effectively identifies similar gene expression changes between studies. This method outperforms traditional Two One-Sided t-Tests (TOST) in detecting equivalent effects from different exposures.

Keywords:
differential gene expressiondiverse experimentsequivalence testmolecular markerstudy comparison

More Related Videos

Mapping Bacterial Functional Networks and Pathways in Escherichia Coli using Synthetic Genetic Arrays
14:06

Mapping Bacterial Functional Networks and Pathways in Escherichia Coli using Synthetic Genetic Arrays

Published on: November 12, 2012

46.5K
Following the Dynamics of Structural Variants in Experimentally Evolved Populations
04:52

Following the Dynamics of Structural Variants in Experimentally Evolved Populations

Published on: February 3, 2023

1.0K

Related Experiment Videos

Last Updated: Aug 23, 2025

An Allele-specific Gene Expression Assay to Test the Functional Basis of Genetic Associations
10:17

An Allele-specific Gene Expression Assay to Test the Functional Basis of Genetic Associations

Published on: November 3, 2010

23.0K
Mapping Bacterial Functional Networks and Pathways in Escherichia Coli using Synthetic Genetic Arrays
14:06

Mapping Bacterial Functional Networks and Pathways in Escherichia Coli using Synthetic Genetic Arrays

Published on: November 12, 2012

46.5K
Following the Dynamics of Structural Variants in Experimentally Evolved Populations
04:52

Following the Dynamics of Structural Variants in Experimentally Evolved Populations

Published on: February 3, 2023

1.0K

Area of Science:

  • Bioinformatics
  • Statistical Genetics
  • Molecular Biology

Background:

  • Identifying similar molecular marker impacts from different exposures is crucial for drug development and understanding biological responses.
  • Current statistical methods lack robustness for comparing effect sizes from independent treatment vs. control studies.
  • Developing reliable approaches to assess equivalence in gene expression is essential for comparative biological research.

Purpose of the Study:

  • To propose and evaluate novel statistical approaches for assessing the equivalence of effect sizes between two independent studies.
  • To compare the performance of a bootstrap test of the Equivalent Change Index (ECI) against the Two One-Sided t-Tests (TOST) for gene expression analysis.

Main Methods:

  • Developed a bootstrap test for the Equivalent Change Index (ECI), calculated as a ratio of effect sizes weighted by p-values.
  • Implemented Two One-Sided t-Tests (TOST) directly on the difference in log-fold changes.
  • Conducted simulation studies to compare ECI bootstrap and TOST using sensitivity, specificity, balanced accuracy, and F1-score.
  • Applied both methods to analyze publicly available microarray data (pancreatic cancer) and RNAseq data (smoking vs. vaping).

Main Results:

  • The ECI bootstrap test demonstrated strong performance (F1-score = 0.95), effectively identifying equivalently changed gene expression.
  • TOST proved too conservative and inefficient for detecting equivalent gene expression changes (F1-score = 0).
  • Analysis of pancreatic cancer and smoking/vaping data revealed that ECI identified relevant genes, while TOST identified none.

Conclusions:

  • A bootstrap test of the Equivalent Change Index (ECI) is a promising statistical method for determining similarity in gene differential expression across diverse studies.
  • This approach can effectively identify genes similarly influenced by specific treatments or exposures, aiding in comparative analysis.
  • The ECI bootstrap test offers a statistically robust solution for equivalence testing in gene expression studies.