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:10/13/2017)... ... ... The Visiting Nurse Association (VNA) of Somerset Hills is proud to host ... items from across the nation, this holiday-themed event will raise funds and awareness for ... The boutique will be open Saturday, November 4 (10:00 a.m. – 5:00 p.m.) ...
(Date:10/13/2017)... ... October 13, 2017 , ... Talented host, ... lowdown on sciatica in a new episode of "Success Files," which is an ... and innovation and investigates each subject in-depth with passion and integrity. , Sciatica ...
(Date:10/12/2017)... ... 12, 2017 , ... First Healthcare Compliance (FHC), an industry ... a range of technology and learning solutions at the 68th Annual American Healthcare ... be held October 14–18, 2017 at the Mandalay Bay Resort in Las Vegas, ...
(Date:10/12/2017)... CITY, Fla. (PRWEB) , ... October 12, 2017 , ... ... cold therapy products, announced today the introduction of an innovative new design of the ... multipurpose pad so you get maximum comfort while controlling your pain while using cold ...
(Date:10/12/2017)... ... October 12, 2017 , ... ... has recently contributed a medical article to the newly revamped Cosmetic Town ... article spotlights the hair transplant procedure known as Follicular Unit Extraction ...
Breaking Medicine News(10 mins):
(Date:10/12/2017)... , Oct. 12, 2017 AVACEN Medical , ... company with their  2017 New Product Innovation Award for ... extensive primary and secondary medical device market research by Frost ... its first-to-market OTC, drug-free pain relief product, the AVACEN 100, ... to treating fibromyalgia widespread pain. ...
(Date:10/11/2017)... Texas , Oct. 11, 2017  True ... services, has amplified its effort during National Breast ... about hereditary cancer risks. ... of Clinical Oncology calculated that more than 10 ... have inherited mutations in BRCA1 or BRCA2 and have ...
(Date:10/5/2017)... , Oct. 5, 2017  In response ... of Oral and Maxillofacial Surgeons (AAOMS) released prescribing ... – to be used as a first-line therapy ... Recognizing the ... AAOMS White Paper "Opioid Prescribing: Acute and Postoperative ...
Breaking Medicine Technology: