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Related Concept Videos

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...
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...
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...
Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

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...
DNA Microarrays02:34

DNA Microarrays

Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...
Next-generation Sequencing03:00

Next-generation Sequencing

The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features.

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Related Experiment Video

Updated: May 18, 2026

Pattern-based Search of Epigenomic Data Using GeNemo
06:38

Pattern-based Search of Epigenomic Data Using GeNemo

Published on: October 8, 2017

Spark: a navigational paradigm for genomic data exploration.

Cydney B Nielsen1, Hamid Younesy, Henriette O'Geen

  • 1Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, V5Z 4S6, Canada. cydneyn@bcgsc.ca

Genome Research
|September 11, 2012
PubMed
Summary
This summary is machine-generated.

We developed Spark, an interactive tool to help biologists analyze genome-wide epigenomic data. Spark reveals epigenetic signatures and discovered a new link between YY1 and CTBP2 in human stem cells.

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Area of Science:

  • Genomics
  • Epigenetics
  • Bioinformatics

Background:

  • Biologists face computational challenges with large-scale genomic data analysis.
  • Genome-scale methodologies require advanced computational skills.
  • Existing tools may not adequately support early data exploration for biologists.

Purpose of the Study:

  • To develop an accessible computational tool for biologists to analyze genome-wide epigenomic data.
  • To lower the computational barrier in early data exploration phases.
  • To enable the discovery of novel epigenetic signatures.

Main Methods:

  • Developed Spark, an interactive pattern discovery and visualization approach.
  • Designed Spark specifically for epigenomic data analysis.
  • Utilized Spark for exploring known and novel epigenetic patterns.

Main Results:

  • Spark effectively reveals known epigenetic signatures.
  • Spark identified novel epigenetic signatures.
  • A previously unappreciated binding association between YY1 and CTBP2 was discovered in human embryonic stem cells.

Conclusions:

  • Spark lowers computational barriers for biologists analyzing epigenomic data.
  • Spark facilitates the discovery of significant biological insights from complex datasets.
  • The tool aids in uncovering novel molecular interactions, such as the YY1-CTBP2 association.