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

Comparing Copy Number Variations and SNPs02:26

Comparing Copy Number Variations and SNPs

18.8K
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%...
18.8K
Single Nucleotide Polymorphisms-SNPs01:05

Single Nucleotide Polymorphisms-SNPs

18.4K
A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...
18.4K
The Colonization of Land02:22

The Colonization of Land

37.7K
Changes in the environment of the early Earth drove the evolution of organisms. As prokaryotic organisms in the oceans began to photosynthesize, they produced oxygen. Eventually, oxygen saturated the oceans and entered the air, resulting in an increase in atmospheric oxygen concentration, known as the oxygen revolution approximately 2.3 billion years ago. Therefore, organisms that could use oxygen for cellular respiration had an advantage. More than 1.5 years ago, eukaryotic cells and...
37.7K
Performing a Simple Data Analysis using MS-Excel Function01:17

Performing a Simple Data Analysis using MS-Excel Function

1.1K
Microsoft Excel offers a suite of functions and tools ideal for statistical analysis, making it accessible to students and researchers. This article outlines fundamental Excel functions pivotal for data analysis.
SUM: This function calculates the total sum of a range of values. It's the foundation for aggregating data, essential for determining overall trends and totals in datasets.
AVERAGE: It computes the mean value of a given set of numbers, providing a quick insight into the central...
1.1K
Specific Heat01:16

Specific Heat

67.5K
The specific heat capacity of a substance refers to the energy required to increase the temperature of one gram of that substance by one degree Celcius. Specific heat capacity is often represented in calories (cal), grams (g), and degrees Celsius (oC), but can also be expressed in joules (J), kilograms (kg), and Kelvin (K), among other units.
For example, increasing the temperature of one gram of water by 1°C requires one calorie of heat energy and can be written as 1 cal/g-°C, or...
67.5K
Cell Specific Gene Expression01:58

Cell Specific Gene Expression

16.6K
Multicellular organisms contain a variety of structurally and functionally distinct cell types, but the DNA in all the cells originated from the same parent cells. The differences in the cells can be attributed to the differential gene expression. Liver cells, whose functions include detoxification of blood, production of bile to metabolize fats, and synthesis of proteins essential for metabolism, must express a specific set of genes to perform their functions. Gene expression also varies with...
16.6K

You might also read

Related Articles

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

Sort by
Same author

Mass spectrometry-based proteomics to study gastric carcinogenesis: pathophysiological molecular characterization.

Scientific reports·2026
Same author

APC Mosaicism: The Limited Utility of Ancillary Testing in Normal Colonic Mucosa.

Gastroenterology·2026
Same author

Genome Sequencing of Undiagnosed European Patients Suspected of Hereditary Cancer: Diagnostic Yield and Identification of Candidate Causative Variants.

JCO precision oncology·2026
Same author

Implementing a molecular prescreening strategy for tumors without public NGS access in a cancer center network: Results from the PREICO project.

European journal of cancer (Oxford, England : 1990)·2026
Same author

Sex Differences in Colorectal Tumor-Associated T-cell Responses.

Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology·2026
Same author

Biallelic Germline Inactivation of HROB Causes Primary Gonadal Insufficiency and is Potentially Associated with Colonic Polyposis Predisposition.

American journal of medical genetics. Part A·2026

Related Experiment Video

Updated: Feb 4, 2026

Mapping Alzheimer's Disease Variants to Their Target Genes Using Computational Analysis of Chromatin Configuration
04:41

Mapping Alzheimer's Disease Variants to Their Target Genes Using Computational Analysis of Chromatin Configuration

Published on: January 9, 2020

19.4K

Colon-specific eQTL analysis to inform on functional SNPs.

Victor Moreno1,2,3,4, M Henar Alonso5,6,7, Adrià Closa5,6,7

  • 1Unit of Biomarkers and Susceptibility, Cancer Prevention and Control Program, Catalan Institute of Oncology (ICO), Barcelona, 08908, Spain. v.moreno@iconcologia.net.

British Journal of Cancer
|October 5, 2018
PubMed
Summary
This summary is machine-generated.

This study used expression quantitative trait loci (eQTL) analysis in colon tissues to identify gene associations with colorectal cancer (CRC) risk single nucleotide polymorphisms (SNPs). The findings provide a valuable resource for prioritizing SNPs for functional studies and identifying key genes.

More Related Videos

Detection and Enrichment of Rare Antigen-specific B Cells for Analysis of Phenotype and Function
09:25

Detection and Enrichment of Rare Antigen-specific B Cells for Analysis of Phenotype and Function

Published on: February 16, 2017

12.8K
Three-Dimensional Culture of Murine Colonic Crypts to Study Intestinal Stem Cell Function Ex Vivo
07:46

Three-Dimensional Culture of Murine Colonic Crypts to Study Intestinal Stem Cell Function Ex Vivo

Published on: October 11, 2022

4.0K

Related Experiment Videos

Last Updated: Feb 4, 2026

Mapping Alzheimer's Disease Variants to Their Target Genes Using Computational Analysis of Chromatin Configuration
04:41

Mapping Alzheimer's Disease Variants to Their Target Genes Using Computational Analysis of Chromatin Configuration

Published on: January 9, 2020

19.4K
Detection and Enrichment of Rare Antigen-specific B Cells for Analysis of Phenotype and Function
09:25

Detection and Enrichment of Rare Antigen-specific B Cells for Analysis of Phenotype and Function

Published on: February 16, 2017

12.8K
Three-Dimensional Culture of Murine Colonic Crypts to Study Intestinal Stem Cell Function Ex Vivo
07:46

Three-Dimensional Culture of Murine Colonic Crypts to Study Intestinal Stem Cell Function Ex Vivo

Published on: October 11, 2022

4.0K

Area of Science:

  • Genomics
  • Cancer Genetics
  • Bioinformatics

Background:

  • Genome-wide association studies (GWAS) have identified numerous colorectal cancer (CRC) susceptibility loci.
  • The functional roles and specific genes underlying most identified CRC risk loci remain largely unknown.
  • Expression quantitative trait loci (eQTL) analysis offers a method to functionally annotate single nucleotide polymorphisms (SNPs) associated with disease risk.

Purpose of the Study:

  • To perform detailed eQTL analysis on colon tissues to identify functional associations between SNPs and gene expression.
  • To provide a searchable web resource for exploring SNP-gene associations in colon tissue.
  • To aid in prioritizing SNPs for further functional investigation and identifying genes responsible for CRC risk.

Main Methods:

  • Utilized the R package MatrixEQTL for genome-wide cis- and trans-eQTL analysis.
  • Analyzed 97 colon tumors, paired adjacent normal mucosa, and 47 healthy colon mucosa samples.
  • Employed linear models adjusted for age, gender, and tissue type for expression data analysis.

Main Results:

  • Identified 29,073 significant SNP-gene associations (P < 0.01) in cis-eQTL analysis, corresponding to 363 unique genes.
  • Detected 10,665 significant SNP-gene associations in trans-eQTL analysis, predominantly on the same chromosome and >1 Mb from the gene.
  • Developed a web tool for searching specific SNPs or genes, enabling correlation analysis and tissue type selection.

Conclusions:

  • The developed eQTL resource is valuable for prioritizing SNPs in colorectal cancer susceptibility loci for functional studies.
  • Facilitates the identification of relevant genes underlying GWAS-identified loci.
  • Supports further research into the functional mechanisms of genetic risk in colorectal cancer.