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:6/1/2016)... June 1, 2016 Favorable Government ... Administration and Criminal Identification to Boost Global Biometrics System ... released TechSci Research report, " Global Biometrics Market ... Forecast and Opportunities, 2011 - 2021", the global biometrics ... 2021, on account of growing security concerns across various ...
(Date:5/9/2016)... May 9, 2016 Elevay is ... to expanding freedom for high net worth professionals seeking ... today,s globally connected world, there is still no substitute ... ever duplicate sealing your deal with a firm handshake. ... by taking advantage of citizenship via investment programs like ...
(Date:4/26/2016)... , April 27, 2016 ... "Global Multi-modal Biometrics Market 2016-2020"  report to their ... , The analysts forecast the global ... of 15.49% during the period 2016-2020.  ... of sectors such as the healthcare, BFSI, transportation, ...
Breaking Biology News(10 mins):
(Date:6/27/2016)... --  Ginkgo Bioworks , a leading organism design ... awarded as one of the World Economic Forum,s ... innovative companies. Ginkgo Bioworks is engineering biology to ... in the nutrition, health and consumer goods sectors. ... including Fortune 500 companies to design microbes for ...
(Date:6/24/2016)... (PRWEB) , ... June 24, 2016 , ... While the ... such as the Cary 5000 and the 6000i models are higher end machines that ... the height of the spectrophotometer’s light beam from the bottom of the cuvette holder. ...
(Date:6/23/2016)... ... June 23, 2016 , ... UAS LifeSciences, one of the ... brand, UP4™ Probiotics, into Target stores nationwide. The company, which has been manufacturing ... to its list of well-respected retailers. This list includes such fine stores as ...
(Date:6/23/2016)... A person commits a crime, and the detective ... the criminal down. An outbreak of foodborne illness ... (FDA) uses DNA evidence to track down the bacteria that ... It,s not. The FDA has increasingly used a complex, cutting-edge ... illnesses. Put as simply as possible, whole genome sequencing is ...
Breaking Biology Technology: