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

17.2K
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...
17.2K
Gene Evolution - Fast or Slow?02:05

Gene Evolution - Fast or Slow?

8.4K
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...
8.4K
Gene Evolution - Fast or Slow?02:05

Gene Evolution - Fast or Slow?

3.8K
3.8K
Genomics02:02

Genomics

42.0K
Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
42.0K
Comparing Copy Number Variations and SNPs02:26

Comparing Copy Number Variations and SNPs

19.4K
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%...
19.4K
Genetic Screens02:46

Genetic Screens

5.9K
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...
5.9K

You might also read

Related Articles

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

Sort by
Same author

Deep learning for fast screening and localization of spinal dural arteriovenous fistulas to enhance clinical workflow.

NPJ digital medicine·2026
Same author

Long-range PCR and Nanopore sequencing for localisation and phasing variants: an end-to-end clinical application workflow.

BMC medical genomics·2025
Same author

Prediction model based on gut microbiota as a non-invasive tool for gastric cancer diagnosis.

Applied microbiology and biotechnology·2025
Same author

Characteristics and potential diagnostic value of gut microbiota in ovarian tumor patients.

Scientific reports·2025
Same author

Biallelic <i>SLC13A1</i> loss-of-function variants result in impaired sulfate transport and skeletal phenotypes, including short stature, scoliosis, and skeletal dysplasia.

Genetics in medicine open·2025
Same author

The naples prognostic score as a new predictor for heart failure: A cross-sectional study.

Heart & lung : the journal of critical care·2025

Related Experiment Video

Updated: Apr 18, 2026

JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics
07:28

JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics

Published on: October 19, 2021

3.7K

FastGCN: a GPU accelerated tool for fast gene co-expression networks.

Meimei Liang1, Futao Zhang1, Gulei Jin1

  • 1Institute of Bioinformatics, Zhejiang University, Hangzhou, Zhejiang, RP China, 310058.

Plos One
|January 21, 2015
PubMed
Summary

We developed a fast GPU-accelerated tool for building gene co-expression networks. This method significantly speeds up the analysis of large biological datasets compared to traditional CPU-based approaches.

More Related Videos

Analyzing Multifactorial RNA-Seq Experiments with DiCoExpress
05:22

Analyzing Multifactorial RNA-Seq Experiments with DiCoExpress

Published on: July 29, 2022

4.1K
A Pathway Association Study Tool for GWAS Analyses of Metabolic Pathway Information
05:01

A Pathway Association Study Tool for GWAS Analyses of Metabolic Pathway Information

Published on: July 1, 2020

3.9K

Related Experiment Videos

Last Updated: Apr 18, 2026

JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics
07:28

JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics

Published on: October 19, 2021

3.7K
Analyzing Multifactorial RNA-Seq Experiments with DiCoExpress
05:22

Analyzing Multifactorial RNA-Seq Experiments with DiCoExpress

Published on: July 29, 2022

4.1K
A Pathway Association Study Tool for GWAS Analyses of Metabolic Pathway Information
05:01

A Pathway Association Study Tool for GWAS Analyses of Metabolic Pathway Information

Published on: July 1, 2020

3.9K

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Gene co-expression networks are crucial for understanding gene function and biological pathways.
  • Existing methods for constructing these networks are often slow and inefficient for large-scale datasets.

Purpose of the Study:

  • To develop a user-friendly, accelerated, and optimized tool for constructing gene co-expression networks.
  • To leverage GPU (Graphics Processing Unit) parallel processing for enhanced computational efficiency.

Main Methods:

  • Utilized genetic entropies for efficient preprocessing and filtering of gene expression data.
  • Implemented Pearson correlation coefficient calculation, normalization, and False Discovery Rate control on a GPU.
  • Employed module identification for network construction and compressed the coefficient matrix to save memory.

Main Results:

  • The GPU implementation demonstrated substantial speed improvements over single-thread C/C++ and R implementations.
  • For large datasets (16,000 genes, 590 individuals), GPU acceleration achieved 63-80 times the speed of single-thread R.
  • GPU performance surpassed multi-core CPU implementations as the number of genes increased.

Conclusions:

  • The developed GPU-based tool offers a significant advancement in the speed and efficiency of gene co-expression network construction.
  • This tool is particularly beneficial for analyzing large genomic datasets, enabling faster biological discoveries.