Corporate Banner
Satellite Banner
Informatics
Scientific Community
 
Become a Member | Sign in
Home>News>This Article
  News
Return

A New Generation Visual Browser of the Epigenome

Published: Tuesday, December 24, 2013
Last Updated: Tuesday, December 24, 2013
Bookmark and Share
The software application provides easily interpretable maps from which to analyse and understand the immense volume of epigenetic and genetic data available.

ChroGPS is a software application that serves to facilitate the analysis and understanding of epigenetic data and to extract intelligible information, which can be downloaded free of charge in Bioconductor, a reference repository for biocomputational software. The scientists at the Institute for Research in Biomedicine (IRB Barcelona) describe the uses of the programme in an article published in the journal Nucleic Acids Research, in which they explain that ChroGPS is the answer to a problem that has been dragging on for the last ten years.

In the last 15 years, researchers worldwide have generated a large amount of information about the epigenome: proteins, factors and epigenetic markers which, when bound to DNA, regulate gene expression. Enormous projects such as ENCODE (for humans and mice) or modENCODE (for other lab model systems, such as the fly Drosophilaor the worm C. elegans) have been devoted to collecting these data in order to analyse and interpret them in the framework of genomic data and to form hypotheses about functions and relations. In spite of these efforts, tools are still needed to extract functional and relational information about the epigenome and to present the results in a visual manner, as ChroGPS does.

“With ChroGPS we wanted to integrate epigenetic data with genetic data to reap the great benefits from them and to be able to understand this information. The analyses continue to be extremely complex and the results to be interpreted very unclear,” says Ferran Azorín, head of the Chromatin Structure and Function lab at IRB Barcelona and CSIC researcher professor, who studies epigenomic regulation. “With this tool we have reached the same conclusions as those presented in Nature by researchers working on the modENCODE, but the enormous difference is that instead of seeing the information in hundreds of graphs and figures like in modENCODE, we have achieved a single map,” explains Azorín.

The initiative emerged from dialogue between Azorín’s group, through the PhD student Joan Font-Burgada, and the bioinformatician Òscar Reina, a member of the Biostatistics and Bioinformatics Unit of IRB Barcelona, which was managed by David Rossell at that time.

“ChroGPS is based on the sequential application of two steps: first the generation of distances (or degrees of similarity) between epigenetic components on the basis of several possible measurements that we have developed, and after, in the representation of these distances in the form of bi- o tri-dimensional maps to facilitate their interpretation. For example, they are like visual maps from which distance tables can be drawn up in kilometers between cities,” describes Òscar Reina, one of the developers of the software application.

“The most important thing for us in this first stage has been to present the biological information in a simple but at the same time reliable manner from the point of view of data treatment, for example correcting systematic biases between experiments that can lead to erroneous conclusions,” adds Rossell, who is now at the University of Warwick, in the UK.

Now that the programme is available to the entire community, the researchers contemplate new challenges with ChroGPS. Among his objectives, Ferran Azorín aims to follow the complex transformation of a healthy cell into a cancerous one through tracking the genetic and epigenetic changes that occur. To tackle this project with ChroGPS, the researchers will have to take new steps in statistical and mathematic methods.


Further Information
Access to this exclusive content is for Technology Networks Premium members only.

Join Technology Networks Premium for free access to:

  • Exclusive articles
  • Presentations from international conferences
  • Over 2,500+ scientific posters on ePosters
  • More than 3,700+ scientific videos on LabTube
  • 35 community eNewsletters


Sign In



Forgotten your details? Click Here
If you are not a member you can join here

*Please note: By logging into TechnologyNetworks.com you agree to accept the use of cookies. To find out more about the cookies we use and how to delete them, see our privacy policy.

Related Content

Finding Could Revolutionize Drug Discovery
A study by researchers at IRB Barcelona reveals the existence of information highways that connect and correlate distant sites within a single protein.
Friday, June 13, 2014
Scientific News
Searching Big Data Faster
Theoretical analysis could expand applications of accelerated searching in biology, other fields.
Imaging Software Could Speed Breast Cancer Diagnosis
Technology could improve access to diagnostic services in developing countries.
Data Mining DNA For Polycystic Ovary Syndrome Genes
A new Northwestern Medicine genome-wide association study of PCOS – the first of its kind to focus on women of European ancestry – has provided important new insights into the underlying biology of the disorder.
Firefly Protein Enables Visualization of Roots in Soil
A new imaging tool from a team led by Carnegie’s José Dinneny allows researchers to study the dynamic growth of root systems in soil, and to uncover the molecular signaling pathways that control such growth.
UEA Research Could Help Build Computers From DNA
New research from the University of East Anglia could one day help build computers from DNA.
Viral Comparisons
ORNL team applies genomics expertise to analyze, map virus sequence database.
Preserving Fleeting Digital Information with DNA
A team has demonstrated that DNA they encapsulated can preserve information for at least 2,000 years, and they’re now working on a filing system to make it easier to navigate.
TGAC Leads Development to Diminish Threat to Vietnam’s Most Important Crop
Advanced bioinformatics capabilities for next-generation rice genomics in Vietnam to aid precision breeding.
Mass Extinctions Can Accelerate Evolution
A computer science team at The University of Texas at Austin has found that robots evolve more quickly and efficiently after a virtual mass extinction modeled after real-life disasters such as the one that killed off the dinosaurs.
Furthering Data Analysis of Next-gen Sequencing to Facilitate Research
Researchers at Cincinnati Children's Hospital Medical Center have developed a user-friendly, integrated platform for analyzing the transcriptomic and epigenomic "big data.
Scroll Up
Scroll Down
Skyscraper Banner

Skyscraper Banner
Go to LabTube
Go to eposters
 
Access to the latest scientific news
Exclusive articles
Upload and share your posters on ePosters
Latest presentations and webinars
View a library of 1,800+ scientific and medical posters
2,500+ scientific and medical posters
A library of 2,500+ scientific videos on LabTube
3,700+ scientific videos
Close
Premium CrownJOIN TECHNOLOGY NETWORKS PREMIUM FREE!