Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

New software for the visual analysis of genome-wide expression data

05.10.2010
Biologists use modern high-density micro arrays to measure the genome-wide expression of exons, the essential parts of alternatively spliced genes.

In particular, exons of many genes encode protein variants involved with important cellular processes. While the measured differences between the variants are often quite small, their distinct biological effects can be profound. Protein variants from the same gene might even have opposing functional consequences.

Therefore, scientists from the Max Planck Institute for Informatics, Saarbrücken, Germany, and the Gladstone Institute of Cardiovascular Disease, San Francisco, CA, USA, developed innovative software to analyze exon expression data.

The new software package for the analysis of the massive data generated by exon micro arrays consists of the programs AltAnalyze (http://www.altanalyze.org) and DomainGraph (http://www.domaingraph.de) and is amenable even to biologists without programming knowledge and experience in bioinformatics. It is the first software that allows researchers not only to perform statistical data analysis, but also to evaluate the biological implications of alternative splicing on cellular processes.

“Once we realized the need for the joint statistical and visual analysis of this type of expression data, we decided to combine our efforts and work towards a free software product that would be both user-friendly and comprehensive in its scope,” says Mario Albrecht, research group leader at the Max Planck Institute and this year’s recipient of the international HUPO Early Career Investigator Award for outstanding young proteome researchers.

The conceptual aim of the software is to provide researchers with an easily accessible way of producing and interpreting statistical results for their large expression data files. Thus, the analysis results can be visualized in the context of molecular networks and pathways, supporting different levels of molecular details so that the biological user is not overwhelmed by the data deluge. “Rather than just providing statistical results as long and cryptic tables, our software empowers users to visually explore the functional consequences of the identified protein variants in mammalian cells. Researchers can readily study the resulting biological differences such as altered protein function and pathway interactions together with the measured exon expression values,” explains Dorothea Emig, research scientist at the Max Planck Institute.

“While mainstream biology has embraced the analysis of gene expression, the extent of alternative splicing has not been researched yet at genomic scale. However, this basic mechanism can have tremendous influence on how cells respond under normal conditions and disease. Our software tools help bringing this kind of science to the forefront of biology research,” adds her cooperation partner Nathan Salomonis, postdoctoral fellow at the Gladstone Institute.

Recently, this software provided Salomonis and colleagues with new predictions on protein variant functioning and targeting by small inhibitory RNAs, which were further validated in embryonic stem cells. “With the software results in hand, the user is presented with functional hypotheses that can be readily tested in further lab experiments. They will have a much greater likelihood of being relevant to the molecular processes of interest”, notes Bruce Conklin, senior investigator at the Gladstone Institute and professor of medical genetics at the University of California, San Francisco.

Original publications:
D. Emig, N. Salomonis, J. Baumbach, T. Lengauer, B.R Conklin, M. Albrecht (2010) AltAnalyze and DomainGraph: analyzing and visualizing exon expression data. Nucleic Acids Res., 38:W755-762, DOI: 10.1093/nar/gkq405.

N. Salomonis, C.R. Schlieve, L. Pereira, C. Wahlquist, A. Colas, A.C. Zambon, K. Vranizan, M.J. Spindler, A.R. Pico, M.S. Cline, T.A. Clark, A. Williams, J.E. Blume, E. Samal, M. Mercola, B.J. Merrill, B.R. Conklin (2010) Alternative splicing regulates mouse embryonic stem cell pluripotency and differentiation. Proc. Natl. Acad. Sci. USA, 107:10514-10519, DOI: 10.1073/pnas.0912260107.

Contact:
Dr. Mario Albrecht
Max Planck Institute for Computer Science
Campus E1.4
66123 Saarbrücken
Germany
Tel.: +49-681-9325-327
Fax: +49-681-9325-399
E-Mail: mario.albrecht@mpi-inf.mpg.de
WWW: http://medbioinf.mpi-inf.mpg.de
Samir Hammann
Max Planck Institute for Computer Science
Campus E1.4
66123 Saarbrücken
Germany
Tel: +49-681-9325-454
E-Mail: s.hammann@mpi-inf.mpg.de

Samir Hammann | Max-Planck-Institut
Further information:
http://medbioinf.mpi-inf.mpg.de

More articles from Information Technology:

nachricht Ultra-precise chip-scale sensor detects unprecedentedly small changes at the nanoscale
18.01.2017 | The Hebrew University of Jerusalem

nachricht Data analysis optimizes cyber-physical systems in telecommunications and building automation
18.01.2017 | Fraunhofer-Institut für Algorithmen und Wissenschaftliches Rechnen SCAI

All articles from Information Technology >>>

The most recent press releases about innovation >>>

Die letzten 5 Focus-News des innovations-reports im Überblick:

Im Focus: How gut bacteria can make us ill

HZI researchers decipher infection mechanisms of Yersinia and immune responses of the host

Yersiniae cause severe intestinal infections. Studies using Yersinia pseudotuberculosis as a model organism aim to elucidate the infection mechanisms of these...

Im Focus: Interfacial Superconductivity: Magnetic and superconducting order revealed simultaneously

Researchers from the University of Hamburg in Germany, in collaboration with colleagues from the University of Aarhus in Denmark, have synthesized a new superconducting material by growing a few layers of an antiferromagnetic transition-metal chalcogenide on a bismuth-based topological insulator, both being non-superconducting materials.

While superconductivity and magnetism are generally believed to be mutually exclusive, surprisingly, in this new material, superconducting correlations...

Im Focus: Studying fundamental particles in materials

Laser-driving of semimetals allows creating novel quasiparticle states within condensed matter systems and switching between different states on ultrafast time scales

Studying properties of fundamental particles in condensed matter systems is a promising approach to quantum field theory. Quasiparticles offer the opportunity...

Im Focus: Designing Architecture with Solar Building Envelopes

Among the general public, solar thermal energy is currently associated with dark blue, rectangular collectors on building roofs. Technologies are needed for aesthetically high quality architecture which offer the architect more room for manoeuvre when it comes to low- and plus-energy buildings. With the “ArKol” project, researchers at Fraunhofer ISE together with partners are currently developing two façade collectors for solar thermal energy generation, which permit a high degree of design flexibility: a strip collector for opaque façade sections and a solar thermal blind for transparent sections. The current state of the two developments will be presented at the BAU 2017 trade fair.

As part of the “ArKol – development of architecturally highly integrated façade collectors with heat pipes” project, Fraunhofer ISE together with its partners...

Im Focus: How to inflate a hardened concrete shell with a weight of 80 t

At TU Wien, an alternative for resource intensive formwork for the construction of concrete domes was developed. It is now used in a test dome for the Austrian Federal Railways Infrastructure (ÖBB Infrastruktur).

Concrete shells are efficient structures, but not very resource efficient. The formwork for the construction of concrete domes alone requires a high amount of...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

12V, 48V, high-voltage – trends in E/E automotive architecture

10.01.2017 | Event News

2nd Conference on Non-Textual Information on 10 and 11 May 2017 in Hannover

09.01.2017 | Event News

Nothing will happen without batteries making it happen!

05.01.2017 | Event News

 
Latest News

A big nano boost for solar cells

18.01.2017 | Power and Electrical Engineering

Glass's off-kilter harmonies

18.01.2017 | Materials Sciences

Toward a 'smart' patch that automatically delivers insulin when needed

18.01.2017 | Life Sciences

VideoLinks
B2B-VideoLinks
More VideoLinks >>>