Navigation Links
Genomatix integrates genome-wide open chromatin from next generation sequencing
Date:2/25/2008

Genomatix Software GmbH, a Systems Biology company focussed on high quality annotation and the understanding of gene regulation, has begun showcasing its abilities in the analysis of data generated by Next Generation Sequencing (NGS) technology.

Allan P. Boyle et al published in the January 2008 issue of Cell some remarkable work on High-Resolution Mapping and Characterization of Open Chromatin across the Genome where they identified DNase I hypersensitive sites from primary human CD4+ Cells. Those samples were sequenced using both the Illumina Solexa and Roche 454 NGS platforms.

Genomatix applied its NGS analysis pipeline to the Illumina Solexa data as deposited at the Gene Expression Omnibus and made the results publicly available.

Out of the roughly 15 million 20mer sequence tags, the Genomatix proprietary ultra fast mapping capability delivered over 11 million (75%) unique positions in less than two hours, allowing up to three point mutations and two insertions/deletions.

Effective noise filtering was performed by sequence tag clustering at different levels of stringency. Genome wide correlation studies show that the majority of open chromatin is located in intergenic and intronic regions.

Additionally a strong correlation is shown between open chromatin and the Genomatix promoter annotation. Distance correlations of sequence tags and transcriptional start sites give further experimental confirmation to the longstanding Genomatix definition of a proximal promoter, spanning from -500 base pairs from TSS to + 100 base pairs downstream of TSS. The analyses show the frequent use of alternative promoters for alternative transcripts within the same gene locus, as postulated by Genomatix since its first genome wide promoter annotations in 2000.

Genomic localization of identified sequences in context with other genomic annotations like transcripts, promoters, TSS, microRNAs, etc. can be accessed by all Genomatix customers and subscribers to a no charge evaluation account to the ElDorado extended genome annotation database.

Dr. Martin Seifert, Vice President Business Development and Consulting at Genomatix says: We are excited about the power and wealth of all the new data being delivered by NGS technology. We have everything in place to analyze all these data and integrate them into our ElDorado annotation database todaysomething we can do within hours of starting an analysis. The real value is realized by overlaying and correlating all this data that has been derived by different approaches, for example, the open chromatin data correlated with chromatinIP tags for several nuclear receptors, expression profiles, microRNAs and all the wealth of other information in our databases that give an excellent handle on localizing and elucidating the role of enhancers/repressors in intergenic regions.

Dr. Seifert continues: Several in-house projects which we conducted for customers demonstrate the clear superiority of our rich data content, our proprietary approaches, and open and modular architecture. With the emergence of NGS, the outstanding value of our technology is now more evident than ever!


'/>"/>

Contact: Klaus May
may@genomatix.de
49-895-997-660
Genomatix Software GmbH
Source:Eurekalert

Related medicine news :

1. Genomatix takes a lead in Next Generation Sequencing
2. Sanofi-Aventis renews licenses for Genomatix chip analysis pipeline
3. NIH/NCI renews and extends nationwide license for Genomatix software and databases
4. Professional Products, Inc. Integrates Clinical Skills and Simulation Center at the Johns Hopkins Hospital
5. Hays AG Integrates Authentidate(R) Signature Solution for Electronic Invoicing
6. Genome-wide survey nets key melanoma gene
7. Researchers provide genetic associations from a genome-wide scan for cardiovascular disease traits
8. Chromatin remodeling complex connected to DNA damage control
9. Off-Label Avastin Use for Wet Macular Degeneration
10. Merging discovery with therapy: Second generation memory care debuts
11. PrimeWest Health Chooses Healthations AboveHealth as Next Generation Provider Portal
Post Your Comments:
*Name:
*Comment:
*Email:
(Date:5/31/2016)... ... 31, 2016 , ... To meet a growing demand for ... The University of Scranton is adding a Certificate in Health Informatics to its ... rapidly growing field of healthcare information. , Healthcare organizations are under growing ...
(Date:5/30/2016)... ... 30, 2016 , ... As the CDC relaxes its stance on traditional No-Nit ... keep their households lice free. , According to a May 26 article from ... kids in the classroom despite the fact that they may be harboring an infestation. ...
(Date:5/30/2016)... ... May 30, 2016 , ... Shaolin Institute officially starts the ... special intensive summer training camp starts on June 17th on Shaolin Institute Atlanta ... children a fun and unique experience with an opportunity to learn KungFu martial ...
(Date:5/29/2016)... ... May 29, 2016 , ... Whole Health Supply is happy to ... KP-240L clipper is available to the public. This is an unusual clipper because it ... the average clipper. , Everything about this product is concentrated on ease of use, ...
(Date:5/28/2016)... (PRWEB) , ... May 28, 2016 , ... "Color Grading ... drag and drop a preset onto their media," said Christina Austin - CEO of ... Studios, editors can quickly and easily add stylish color grades to their footage. A ...
Breaking Medicine News(10 mins):
(Date:5/30/2016)... , May 30, 2016 On ... eliminate viral hepatitis by 2030. At the 69 th ... ever Global Viral Hepatitis Strategy, signalling the greatest global commitment ... a goal of eliminating hepatitis B and C by 2030 ... if reached, will reduce annual deaths by 65% and increase ...
(Date:5/27/2016)... 27, 2016  A new study highlights the necessity of health literacy within the ... the American College of Radiology , a majority of oncology patients undergo imaging screenings ... http://photos.prnewswire.com/prnh/20160527/373022 ... ... Medical Diagnostic Imaging Ampronix ...
(Date:5/27/2016)... 27, 2016 Kitov ... focused on late-stage drug development, today announced the ... of pivotal batches required for registration of KIT-302 ... This follows Kitov,s announcement in December ... met its primary efficacy endpoint. "We ...
Breaking Medicine Technology: