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

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
'/>"/>

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

Page: 1 2 3

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:7/10/2014)... CORAL SPRINGS, Florida , July 1, 2014 ... smart wallets pave way for convenience and improved security: NXT-ID, ... Google Inc. (NASDAQ: GOOG ), Apple Inc. (NASDAQ: ... ) and MasterCard Corporation (NYSE: MA) NXT-ID, Inc., (OTCQB: ... market, is pleased to announce that the second series of ...
(Date:7/10/2014)... 2, 2014 It is a great honor ... appointment of the world-renowned Thoracic and Cardiovascular surgeon, Mark ... Dr. Ginsburg, with over 34 years of experience, ... and Good Samaritan Regional Medical Center. Dr. Ginsburg has ... 1980,s and is considered an expert in the implantation ...
(Date:7/10/2014)... According to the new market research report, ... (Optical Prism, Pizeoelectric, Capacitive, and Adhesives), Application (Mobile Devices, ... and Geography - Global Trends & Forecasts to 2014 ... Market is projected to cross $14.35 Billion by 2020, ... to 2020. Browse more than 78 market ...
Breaking Biology News(10 mins):Advantages for Digital Wallets Eliminate Need to Carry Credit Cards - Large Scale CNBC Ad Campaign for Latest Smart Wallet to Commence July 7th 2Advantages for Digital Wallets Eliminate Need to Carry Credit Cards - Large Scale CNBC Ad Campaign for Latest Smart Wallet to Commence July 7th 3Advantages for Digital Wallets Eliminate Need to Carry Credit Cards - Large Scale CNBC Ad Campaign for Latest Smart Wallet to Commence July 7th 4Advantages for Digital Wallets Eliminate Need to Carry Credit Cards - Large Scale CNBC Ad Campaign for Latest Smart Wallet to Commence July 7th 5Avery Biomedical Devices, Inc. announces the appointment of Mark E Ginsburg, M.D. to its Board of Directors 2Fingerprint Sensors Market worth $14.35 Billion by 2020 2Fingerprint Sensors Market worth $14.35 Billion by 2020 3
... Aug. 28 Gamma globulin, a type of antibody ... given to health care workers and international travelers to ... treatment for pinkeye with little apparent toxicity, according to ... School of Medicine. The results of the study, being ...
... prevalent cancers in the Western world. The tumor starts off ... violent cancer, which often spreads to the liver. In an ... Ben-Zeev and Dr. Nancy Gavert of the Weizmann Institutes Molecular ... In a majority of cases, colorectal cancer is initiated ...
... of Pennsylvania researchers have designed a nanoscale system ... to external forces. By combining microfabricated ... nanoscale sensors, the study showed that cells respond ... relationship between cells and their environment. The study ...
Cached Biology News:Gamma globulin effective in treating eye infections caused by adenoviruses 2A gene for metastasis 2Bioengineers at University of Pennsylvania devise nanoscale system to measure cellular forces 2
(Date:7/10/2014)... April 15, 2014 -- According to the International ... nuclear security comes from terrorists acquiring sufficient quantities ... construct a crude nuclear explosive device. The IAEA ... trafficking have involved gram-level quantities, which can be ... According to a new study appearing this week ...
(Date:7/10/2014)... in the journal PNAS (Proceedings of the National ... day and sleep deprivation have a significant effect on ... at the best time of day to test for ... administering medicines effectively. , Researchers from the University of ... the links between sleep deprivation, body clock disruption and ...
(Date:7/10/2014)... The lithium-ion batteries that power our laptops and ... on a single charge with the help of a ... material to replace the graphite traditionally used in one ... 10 times the energy storage capacity of graphite. A ... electrode was published today in Nature Communications . ...
(Date:7/10/2014)... at the University of Illinois at Urbana-Champaign provides ... interplay of spin and heat at the nanoscale, ... devices for data storage and information processing. ... spin-angular momentum. In a typical charge current, electrons, ... current," explained David Cahill, a professor of materials ...
Breaking Biology Technology:Sensitive detection method may help impede illicit nuclear trafficking 2Time of day crucial to accurately test for diseases, new research finds 2Silicon sponge improves lithium-ion battery performance 2Silicon sponge improves lithium-ion battery performance 3University of Illinois study advances limits for ultrafast nano-devices 2
... Assembly Speaker Mike Huebsch , R-West Salem, and State ... to serve on the Speaker's Task Force on Information Technology ... a number of failed information technology projects in state government, ... sectors. , ,In addition to Montgomery, who will serve as ...
... we will often hear, Oh, about 11,000 hours. , ... another 11,000-hour project that was canceled without producing any software? ... bitof software, but software that was extremely profitable? There's an ... of software, we're left with hand waving. , ,Hand waving ...
... 10th in a series of articles on developing start-up companies ... Madison, Wis. - In Step 9 we discussed ... specifically on the federal laws. , ,Any business that ... federal securities laws and regulations. Of equal importance are the ...
Cached Biology Technology:Eight lawmakers named to Speaker's IT task force 2Defining the X-factor: What is an ounce of software worth? 2Defining the X-factor: What is an ounce of software worth? 3Defining the X-factor: What is an ounce of software worth? 4Early Stage 10: The nuances of federal laws 2Early Stage 10: The nuances of federal laws 3Early Stage 10: The nuances of federal laws 4Early Stage 10: The nuances of federal laws 5