Navigation Links
New annotated database sifts through mountains of sequencing data to find gene promoters
Date:12/22/2010

Researchers at The Wistar Institute announce the release of an online tool that will help scientists find "gene promoters"regions along a DNA strand that tell a cell's transcription machinery where to start reading in order to create a particular protein. The Mammalian Promoter Database (MPromDb) integrates the genome sequencing data generated at Wistar with publicly available data on human and mouse genomics. MPromDb pinpoints known promoters and predicts where new ones are likely to be found, the researchers say.

"Several complete genome sequences are available, including highly accurate assembled sequences from more than 1,000 individuals from the '1000 Genome Project,' with the goal of providing a comprehensive resource on human genetic variation and guiding us into the personal genomics era," said Ramana V. Davuluri, Ph.D., associate professor in Wistar's Molecular and Cellular Oncogenesis Program and associate director of The Wistar Institute Center for Systems and Computational Biology. "With this information, researchers can design personalized diagnostics and therapeutics or delve deeper into the study of gene regulation than previously thought possible."

Davuluri and his colleagues published details of how they built MPromDb in the journal Nucleic Acids Research, available online now.

Contrary to what was once the textbook view of genetics, one gene may not encode just one protein. In fact, scientists now know that a single gene may encode multiple versions of a given proteincalled a protein's isoformswhich allows cells to make almost 100,000 distinct proteins even though our DNA only encodes about 20,000 protein-coding genes. As the body grows in the womb, cells may use different isoforms at different stages of development. Likewise, different adult cells may also use different isoforms of a protein depending on what type of cell it is, such as a neuron versus a skin cell.

"We have evolved this beautiful system where our DNA creates tremendous diversity from a limited set of genetic instructions," Davuluri said. "Recent evidence shows that at least half of all of our genes have alternative promoters that allow cells to make transcript variants and protein isoforms."

Earlier reports from the Davuluri laboratory showed that nearly 40 percent of genes use alternative promoters to create protein isoforms. According to Davuluri, integrating this information with data from other studies would surely find significantly more of these alternative promoters.

"Much of the genetic variations occur outside protein coding regions, such as gene regulatory regions," Davuluri said. "MPromDb provides context for data in the form of gene promoter annotations that can tell you where and when our bodies make a particular protein variant."

MPromDb mines its information from huge databases maintained by national and international consortiums of researchers, such as Gene Expression Omnibus (GEO) maintained by the National Center for Biotechnology Information and ENCyclopedia of DNA Elements (ENCODE) run by the National Human Genome Research Institute. Essentially, MPromDb looks for key DNA sequences that could be potential binding sites for Polymerase II, an enzyme that creates the RNA transcript that the cell later translates into protein. The current database contains information on over 42,000 human promoters found in six different cell types and over 48,000 mouse gene promoters found in 10 different cell types.

"In fact, scientists are so good at generating this sort of information using next generation sequencing methods, that they collect information far in excess of what they might need for a given experiment or project," Davuluri said. "This information all ends up in places like GEO, waiting to be discovered by groups like ours."

According to Davuluri, the Wistar Center for Systems and Computational Biology plans to expand MPromDb to include epigenetic datainformation on modifications to DNA that affect gene regulation; protein-DNA interaction data; and genetic variation data for both humans and mice.


'/>"/>

Contact: Greg Lester
glester@wistar.org
215-898-3943
The Wistar Institute
Source:Eurekalert

Related biology news :

1. Bird call database nests online
2. NEWMEDS announces new drug database
3. Unique database of cancer -- designed to personalize treatment -- is launched
4. What the doctor prescribes: Customized medical-image databases
5. UC Riverside entomologist to oversee centralized database of bee specimens
6. Developer of DNA barcode database wins Ebbe Nielsen Prize
7. Nations largest organization of ecologists offers expert database
8. Database gives access to the latest findings about the tree of life
9. Penn, Georgia collaboration awarded $14.6 million to expand pathogen database
10. Largest-ever database for liver proteins may lead to treatments for hepatitis
11. Rutgers-Camden developing enzyme function database
Post Your Comments:
*Name:
*Comment:
*Email:
(Date:3/23/2017)... 2017 Research and Markets has announced the ... Trends - Industry Forecast to 2025" report to their offering. ... The Global ... of around 8.8% over the next decade to reach approximately $14.21 ... market estimates and forecasts for all the given segments on global ...
(Date:3/22/2017)... 21, 2017 Optimove , provider ... retailers such as 1-800-Flowers and AdoreMe, today announced ... and Replenishment. Using Optimove,s machine learning algorithms, these ... and replenishment recommendations to their customers based not ... of customer intent drawn from a complex web ...
(Date:3/20/2017)... HANOVER, Germany , March 20, 2017 At ... Hamburg -based biometrics manufacturer DERMALOG. The Chancellor came to the ... Japan is this year,s CeBIT partner country. At the largest ... important biometrics in use: fingerprint, face and iris recognition as well as ... ...
Breaking Biology News(10 mins):
(Date:4/20/2017)... -- Dutch philosopher Koert van Mensvoort - founder of the ... Technology in Eindhoven - has written a ,Letter to Humanity, in ... to avoid becoming a slave and victim to its own technology, but to ... ... Koert van Mensvoort – founder of the Next Nature Network and Fellow of ...
(Date:4/19/2017)... ... April 18, 2017 , ... A number of new instruments have ... is part of the Protein and Cell Analysis Education Webinar Series , will ... technology fits in current and future applications. , Many flow cytometers have unique ...
(Date:4/19/2017)... ... April 19, 2017 , ... ThermaGenix, ... round. This event adds to several other early achievements at ThermaGenix, including the ... Teams. , ThermaGenix will use proceeds from the Series A-1 round ...
(Date:4/19/2017)... 19, 2017  As a Bronze Sponsor ... Summit ,  Proove® Biosciences, Inc. announces the ... and lifestyle factors to accurately predict prescription opioid ... Southern California (USC), the Interventional Pain Institute in ... results showing that Proove Opioid Risk® accurately identifies ...
Breaking Biology Technology: