Navigation Links
IRB develops ChroGPS, a new generation visual browser of the epigenome
Date:12/20/2013

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 Drosophila or 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 Azorn, 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 Azorn.

The initiative emerged from dialogue between Azorn's group, through the PhD student Joan Font-Burgada, and the bioinformatician scar 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 scar 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 Azorn 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.


'/>"/>

Contact: Sònia Armengou
armengou@irbbarcelona.org
34-934-037-255
Institute for Research in Biomedicine (IRB Barcelona)
Source:Eurekalert  

Related biology news :

1. Anglo-French partnership develops guidance on future management of English Channel
2. SU biologist develops method for monitoring shipping noise in dolphin habitat
3. QUT develops software to reduce greenhouse gases
4. NTU scientist develops a multi-purpose wonder material to tackle enviromental challenges
5. BGI Tech develops novel Ultra-Deep de novo assembly solution for heterozygous genomes
6. Cleveland Clinic develops clinical screening program for no.1 genetic cause of colon cancer
7. National Heart Centre Singapore develops worlds first human heart cell model
8. AVT Develops Biometrically Secure Medicine Storage and Retrieval System for Medbox RX
9. BGI Tech develops whole exome sequencing analysis of FFPE DNA samples to boost biomedicine
10. IU chemist develops new synthesis of most useful, yet expensive, antimalarial drug
11. MMV develops framework to assess risk of resistance for antimalarial compounds
Post Your Comments:
*Name:
*Comment:
*Email:
Related Image:
IRB develops ChroGPS, a new generation visual browser of the epigenome
(Date:4/19/2016)... , UAE, April 20, 2016 ... implemented as a compact web-based "all-in-one" system solution for ... biometric fingerprint reader or the door interface with integration ... modern access control systems. The minimal dimensions of the ... readers into the building installations offer considerable freedom of ...
(Date:3/31/2016)...   LegacyXChange, Inc. ... LegacyXChange is excited to release its first ... be launched online site for trading 100% guaranteed authentic ... also provide potential shareholders a sense of the value ... industry that is notorious for fraud. The video is ...
(Date:3/22/2016)... PROVO and SANDY, ... Screening Ontario (NSO), which operates the highest sample volume ... testing, and Tute Genomics and UNIConnect, leaders in clinical ... today announced the launch of a project to establish ... testing panel. NSO has been contracted ...
Breaking Biology News(10 mins):
(Date:4/28/2016)... , ... April 28, 2016 , ... ... will deliver a talk on its first-in-class technologies for tissue stem cell ... Meeting on RNAiMicroRNA Biology to Reprogramming & CRISPR-based Genome Engineering in Burlington, ...
(Date:4/27/2016)... ... 2016 , ... Cambridge Semantics, the leading provider of Smart Data ... has been named to The Silicon Review’s “20 Fastest Growing Big Data Companies of ... serves the needs of end users facing some of the most complex data challenges ...
(Date:4/27/2016)... ... April 27, 2016 , ... Most consumers ... with fingerprint recognition for secure access, voice recognition for hands-free communication, and facial ... are interacting with biometrics technology today. But if they asked Joey Pritikin, ...
(Date:4/27/2016)... British Virgin Islands (PRWEB) , ... April 27, ... ... Holding Company Ltd. (d/b/a Biohaven) is pleased to announce the appointment of John Tilton ... he was an Executive Director and one of the founding commercial leaders responsible ...
Breaking Biology Technology: