Genomatix integrates genome-wide open chromatin from next generation sequencing

February 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 today...something 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!"
-end-
Open chromatin results: http://www.genomatix.de/open_chromatin.html.

Access to the full data within ElDorado for customers or existing free of charge evaluation accounts: http://www.genomatix.de/cgi-bin/sessions/login.pl

Registration to a free of charge evaluation account: http://www.genomatix.de/cgi-bin/UMapps/register.pl

Homepage: www.genomatix.de, www.genomatix-software.com

Original data set: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM252783

For more information or pictures please contact:

research@genomatix.de
Klaus J.W. May
Genomatix Software GmbH
Bayerstr. 85a
D-80335 Munich
Germany
+49-89-599 766 0

info@genomatix-software.com
Peter Grant
Genomatix Software, Inc.
3025 Boardwalk, Suite 160
Ann Arbor, MI 48108
U.S.A.
(877) 436-6628

Genomatix Software GmbH

Related Genome Articles from Brightsurf:

Genome evolution goes digital
Dr. Alan Herbert from InsideOutBio describes ground-breaking research in a paper published online by Royal Society Open Science.

Breakthrough in genome visualization
Kadir Dede and Dr. Enno Ohlebusch at Ulm University in Germany have devised a method for constructing pan-genome subgraphs at different granularities without having to wait hours and days on end for the software to process the entire genome.

Sturgeon genome sequenced
Sturgeons lived on earth already 300 million years ago and yet their external appearance seems to have undergone very little change.

A sea monster's genome
The giant squid is an elusive giant, but its secrets are about to be revealed.

Deciphering the walnut genome
New research could provide a major boost to the state's growing $1.6 billion walnut industry by making it easier to breed walnut trees better equipped to combat the soil-borne pathogens that now plague many of California's 4,800 growers.

Illuminating the genome
Development of a new molecular visualisation method, RNA-guided endonuclease -- in situ labelling (RGEN-ISL) for the CRISPR/Cas9-mediated labelling of genomic sequences in nuclei and chromosomes.

A genome under influence
References form the basis of our comprehension of the world: they enable us to measure the height of our children or the efficiency of a drug.

How a virus destabilizes the genome
New insights into how Kaposi's sarcoma-associated herpesvirus (KSHV) induces genome instability and promotes cell proliferation could lead to the development of novel antiviral therapies for KSHV-associated cancers, according to a study published Sept.

Better genome editing
Reich Group researchers develop a more efficient and precise method of in-cell genome editing.

Unlocking the genome
A team led by Prof. Stein Aerts (VIB-KU Leuven) uncovers how access to relevant DNA regions is orchestrated in epithelial cells.

Read More: Genome News and Genome Current Events
Brightsurf.com is a participant in the Amazon Services LLC Associates Program, an affiliate advertising program designed to provide a means for sites to earn advertising fees by advertising and linking to Amazon.com.