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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...
Genomics02:02

Genomics

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...
Genome Size and the Evolution of New Genes03:21

Genome Size and the Evolution of New Genes

While every living organism has a genome of some kind (be it RNA, or DNA), there is considerable variation in the sizes of these blueprints. One major factor that impacts genome size is whether the organism is prokaryotic or eukaryotic. In prokaryotes, the genome contains little to no non-coding sequence, such that genes are tightly clustered in groups or operons sequentially along the chromosome. Conversely, the genes in eukaryotes are punctuated by long stretches of non-coding sequence.
Genome Size and the Evolution of New Genes03:21

Genome Size and the Evolution of New Genes

While every living organism has a genome of some kind (be it RNA, or DNA), there is considerable variation in the sizes of these blueprints. One major factor that impacts genome size is whether the organism is prokaryotic or eukaryotic. In prokaryotes, the genome contains little to no non-coding sequence, such that genes are tightly clustered in groups or operons sequentially along the chromosome. Conversely, the genes in eukaryotes are punctuated by long stretches of non-coding sequence.
Genetic Screens02:46

Genetic Screens

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 result in visible changes...
Reporter Genes02:11

Reporter Genes

Reporter genes are a type of protein-coding gene that are often tagged to a gene of interest. Once inside a target cell, reporter genes usually produce visually identifiable characteristics like fluorescence and luminescence when expressed along with the gene of interest. Thus, reporter genes “report” the presence or absence of genes of interest in an organism, determine the gene expression pattern, or track the physical location of a DNA segment or protein in the cell.
Commonly used reporter...

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Related Experiment Video

Updated: Jun 19, 2026

A Protocol for Using Gene Set Enrichment Analysis to Identify the Appropriate Animal Model for Translational Research
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Published on: August 16, 2017

GeneShelf: a web-based visual interface for large gene expression time-series data repositories.

Bohyoung Kim1, Bongshin Lee, Susan Knoblach

  • 1Seoul National University. bhkim@cse.snu.ac.kr

IEEE Transactions on Visualization and Computer Graphics
|October 17, 2009
PubMed
Summary

GeneShelf is a new web-based visual interface designed to improve the exploration of gene expression datasets. It offers interactive features for biologists to better analyze complex biological data.

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Last Updated: Jun 19, 2026

A Protocol for Using Gene Set Enrichment Analysis to Identify the Appropriate Animal Model for Translational Research
09:35

A Protocol for Using Gene Set Enrichment Analysis to Identify the Appropriate Animal Model for Translational Research

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Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine
10:40

Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine

Published on: December 22, 2017

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • High-throughput gene expression analysis generates vast datasets.
  • Public databases store gene expression data but offer limited interactivity.
  • Biologists need improved tools to explore complex gene expression datasets.

Purpose of the Study:

  • To design and develop GeneShelf, a novel web-based visual interface.
  • To enhance the exploration and utility of public gene expression datasets.
  • To address the limitations of static data representations in current repositories.

Main Methods:

  • Developed GeneShelf, a web-based visual interface.
  • Utilized a zoomable grid display for two categorical dimensions.
  • Incorporated an augmented timeline with expandable time points and embedded bar charts.
  • Applied GeneShelf to a large microarray dataset of spinal cord injury in mice and rats.

Main Results:

  • GeneShelf provides an interactive platform for gene expression data exploration.
  • The interface effectively visualizes multiple data values at focused time points.
  • A case study and user study demonstrated GeneShelf's utility and usability.

Conclusions:

  • GeneShelf offers a significant improvement over static gene expression data repositories.
  • The developed interface enhances biologists' ability to explore and interpret complex datasets.
  • GeneShelf shows promise for advancing research in fields utilizing gene expression analysis.