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

Genome-wide Association Studies-GWAS01:11

Genome-wide Association Studies-GWAS

Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
GWAS does not require the identification of the target gene involved in...
Genome Annotation and Assembly03:36

Genome Annotation and Assembly

The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
Protein Networks02:26

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
Protein Networks02:26

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
Gene Families01:57

Gene Families

Gene families consist of groups of genes proposed to have originated from a common ancestor. Typically these arise through events in which a gene or genes are mistakenly duplicated during cell division. Unlike their parent genes (which are subject to selection pressure to maintain function), these gene copies do not need to preserve their sequences and may evolve at a relatively faster rate.
Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...
Gene Families01:57

Gene Families

Gene families consist of groups of genes proposed to have originated from a common ancestor. Typically these arise through events in which a gene or genes are mistakenly duplicated during cell division. Unlike their parent genes (which are subject to selection pressure to maintain function), these gene copies do not need to preserve their sequences and may evolve at a relatively faster rate.
Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...

You might also read

Related Articles

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

Sort by
Same author

In vivo roles for myosin phosphatase targeting subunit-1 phosphorylation sites T694 and T852 in bladder smooth muscle contraction.

The Journal of physiology·2014
Same author

High-temperature cultivation of recombinant Pichia pastoris increases endoplasmic reticulum stress and decreases production of human interleukin-10.

Microbial cell factories·2014
Same author

Metabolic engineering of strains: from industrial-scale to lab-scale chemical production.

Journal of industrial microbiology & biotechnology·2014
Same author

Inhibition of histone deacetylase by butyrate protects rat liver from ischemic reperfusion injury.

International journal of molecular sciences·2014
Same author

[Determination of arsenic speciation in Scomberomorus niphonius by capillary electrophoresis-inductively coupled plasma mass spectrometry].

Guang pu xue yu guang pu fen xi = Guang pu·2014
Same author

Regulation of CRADD-caspase 2 cascade by histone deacetylase 1 in gastric cancer.

American journal of translational research·2014

Related Experiment Video

Updated: May 28, 2026

Annotation of Plant Gene Function via Combined Genomics, Metabolomics and Informatics
08:09

Annotation of Plant Gene Function via Combined Genomics, Metabolomics and Informatics

Published on: June 17, 2012

A novel method to quantify gene set functional association based on gene ontology.

Sali Lv1, Yan Li, Qianghu Wang

  • 1College of Bioinformatics Science and Technology and Bio-pharmaceutical Key Laboratory of Heilongjiang Province, Harbin Medical University, Harbin, People's Republic of China.

Journal of the Royal Society, Interface
|October 15, 2011
PubMed
Summary

We developed a new method to measure functional similarity between gene sets, aiding complex disorder research. This tool, Gene Set Functional Similarity (GSFS), improves understanding of gene relationships and experimental reproducibility.

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

Related Experiment Videos

Last Updated: May 28, 2026

Annotation of Plant Gene Function via Combined Genomics, Metabolomics and Informatics
08:09

Annotation of Plant Gene Function via Combined Genomics, Metabolomics and Informatics

Published on: June 17, 2012

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

Area of Science:

  • Genomics
  • Bioinformatics
  • Systems Biology

Background:

  • Gene sets are crucial molecular signatures for complex disorder research.
  • Comparing gene sets aids in evaluating experimental reproducibility and understanding biological function.
  • Existing methods for gene set comparison have limitations in accurately reflecting functional associations.

Purpose of the Study:

  • To improve the measurement of semantic similarity for quantifying functional associations between gene sets.
  • To develop a web toolkit, Gene Set Functional Similarity (GSFS), for assessing functional similarity.
  • To validate the GSFS method and compare its performance against existing approaches.

Main Methods:

  • Developed an improved semantic similarity measurement within the Gene Ontology (GO) framework.
  • Created the Gene Set Functional Similarity (GSFS) web toolkit.
  • Validated GSFS using protein complexes and compared it with pairwise and annotation methods.
  • Conducted case studies on prostate cancer gene expression and coronary heart disease pathways.

Main Results:

  • GSFS scores correlate with sequence similarity and identify complexes within the same functional categories.
  • GSFS demonstrates superior discrimination compared to pairwise and annotation methods.
  • GSFS accurately reflects shared functional catalogues between biological entities.
  • Case studies highlight GSFS's utility in analyzing gene expression data and identifying disease pathways.

Conclusions:

  • The improved semantic similarity measurement and GSFS toolkit effectively quantify functional associations between gene sets.
  • GSFS provides a more accurate and discriminative approach for comparing gene sets in complex disorder research.
  • The GSFS method has significant potential to advance studies on the molecular basis of complex diseases.