Navigation Links
Genomic data are growing, but what do we really know?
Date:3/20/2013

"We live in the post-genomic era, when DNA sequence data is growing exponentially", says Miami University (Ohio) computational biologist Iddo Friedberg. "But for most of the genes that we identify, we have no idea of their biological functions. They are like words in a foreign language, waiting to be deciphered." Understanding the function of genes is a problem that has emerged at the forefront of molecular biology. Many groups develop and employ sophisticated algorithms to decipher these "words". However, until now there was no comprehensive picture of how well these methods perform, "To use the information in our genes to our advantage, we first need to take stock of how well we are doing in interpreting these data".

To do so, Friedberg and his colleagues, Predrag Radivojac, of Indiana University, Bloomington IN and Sean Mooney, Buck Institute for Research on Aging, Novato CA organized the Critical Assessment of protein Function Annotation, or CAFA. CAFA is a community-wide experiment to assess the performance of the many methods used today to predict the functions of proteins, the workhorses of the cell coded by our genes.

Thirty research groups comprising 102 scientists and students participated in CAFA, presented a total of 54 methods. The participating groups came from leading universities in North America, Europe, Asia and Australia. The groups participated in blind-test experiments in which they predicted the function of protein sequences for which the functions are already known but haven't yet been made publicly available. Independent assessors then judged their performance.

The results are published in this month's issue of Nature Methods co-authored by members of all the participating groups, with Friedberg and Radivojac as lead authors. Fifteen companion papers have been published in a special issue of BMC Bioinformatics detailing the methods

"We have discovered a great enthusiasm and community spirit", said Friedberg, who since 2005 has been organizing Automated Function Prediction (AFP) meetings internationally. This, despite the competitive environment in which research groups want their methods to perform better than their peers' methods. Overall, throughout CAFA there was a highly collegial spirit, and a willingness to share information and science. "Everyone recognized that this is an important endeavor, and that only by a group effort can we move the field forward and learn to harness the deluge of genomic data, turning it into useful information."

"For the first time we have broad insight into what works, where improvement is needed, and how we should move the field forward. We will continue running CAFA in the future, as we are confident it will only help generate better methods to understand the information locked in our genomes, and those of other organisms," Friedberg said.

The initial analysis suggests that algorithms combining disparate prediction clues taken from different knowledge-bases provide more accurate predictions. The lead methods combined data from phylogenetic, gene-expression and protein-protein interaction data to provide predictions.


'/>"/>

Contact: Iddo Friedberg
friedbi@miamioh.edu
Miami University
Source:Eurekalert

Related biology news :

1. SDSCs big data expertise aiding genomics research
2. BGI, University of Helsinki and Wuhan University sign a MOU concerning cooperation on genomics
3. In search for a vaccine, IU biologist receives $2.3 million to explore chlamydia genomics
4. 2012 ACMG Foundation/Signature Genomic Laboratories Travel Award winner announced
5. Researchers announce GenomeSpace environment to connect genomic tools
6. ACRG and BGI report findings from genomics research on recurrent hepatitis B virus integration
7. The genomics symposium to boost the further development of cancer research
8. Searching genomic data faster
9. New genomic sequencing method enables smarter anaysis of individual cells
10. Elsevier launches new open access journal: Applied and Translational Genomics
11. ShanghaiBio Corporation Partners with Ingenuity Systems to Address Challenges in Analysis and Interpretation of Genomics Data
Post Your Comments:
*Name:
*Comment:
*Email:
(Date:1/22/2016)... , January 22, 2016 /PRNewswire/ ... announced the addition of the  "Global ... their offering. --> http://www.researchandmarkets.com/research/4lmf2s/global_behavioral ... the  "Global Behavioral Biometric Market 2016-2020" ... Research and Markets ( http://www.researchandmarkets.com/research/4lmf2s/global_behavioral ) ...
(Date:1/20/2016)... Minn. , Jan. 20, 2016   MedNet ... supports the entire spectrum of clinical research, is pleased ... 2015. MedNet,s significant achievements are the result of the ... iMedNet eClinical , it,s comprehensive, easy-to-use ... --> --> Key MedNet growth achievements ...
(Date:1/13/2016)... ALBANY, New York , January 13, 2016 /PRNewswire/ ... Transparency Market Research has published a new market report ... Share, Growth, Trends, and Forecast, 2015 - 2023. According to ... mn in 2014 and is anticipated to reach US$1,625.8 ... from 2015 to 2023. In terms of volume, the ...
Breaking Biology News(10 mins):
(Date:2/6/2016)... Virginia (PRWEB) , ... February 06, 2016 , ... ... E-mail: amitchell(at)cee(dot)org , The Center for Excellence in Education Sponsors Teacher Training ... VA – February 4, 2016 – The Center for Excellence in Education (CEE) ...
(Date:2/5/2016)... 5, 2016 Australian-US drug discovery and development company, ... appointment of a new Chairman, Mr John O,Connor , ... immediately. James Garner , has also been ... former Acting CEO, Mr Iain Ross , will resume ... --> James Garner , has also been formally appointed ...
(Date:2/4/2016)... Falls Church, VA (PRWEB) , ... ... ... a first-year cybersecurity conference presented by Bloomsburg University’s Digital Forensics Club, takes ... Bloomsburg, PA. The two-day event features 20+ speakers and activities such as ...
(Date:2/4/2016)... EDISON, N.J. , Feb. 4, 2016 ... company focused on the development and commercialization of targeted ... BIO CEO & Investor Conference 2016, to be held ... and Source Capital Group,s 2016 Disruptive Growth & Healthcare ... on February 10-11, 2016. James Sapirstein ...
Breaking Biology Technology: