Project leader: Professor SAMUEL KASKI, 
Helsinki University of Technology, Neural Networks Research Centre, P.O. Box 9800, FIN-02015 HUT, Finland +358-9-4518203, samuel.kaski@hut.fi

Project partners: Professor Jonas Blomberg, Section of Virology, Department of Medical Sciences, Uppsala University University Hospital, SE-75185 Uppsala, Sweden

Doctoral students: 
- Merja Oja, University of Helsinki, Department of Computer Science, merja.oja@cs.helsinki.fi Helsinki University of Technology, Neural Networks Research Centre, merja.oja@hut.fi
- Arto Klami University of Helsinki, Department of Computer Science, arto.klami@cs.helsinki.fi Helsinki University of Technology, Neural Networks Research Centre, arto.klami@hut.fi

Key words:  Endogenous retrovirus, bioinformatics, exploratory data analysis, genetic sequence, gene expression

Results

We developed new self-organizing map (SOM) -based methods for organizing, classifying and visualizing genomic sequences. The new means of HERV (Human Endogenous RetroVirus) classification is the main biological outcome so far. New HERV groups, such as the ERV9-like, and epsilonretrovirus-like ones, have been defined. This is of great interest as a basis for understanding HERV evolution and function and, indeed, the evolution and function of the human genome. For the hard but central task of detecting and characterizing of the beginning and end sequences of HERVs, a variant of Hidden Markov Models (HMM) was designed.

Expression of HERVs was studied using newly designed real-time PCRs. This indicated that many HERVs are expressed at the RNA level, which is new information. The involvement of HERVs in diseases like multiple sclerosis and schizophrenia was also studied using the new techniques. Although there are always more things to study, no evidence for an increased expression was found in samples from such patients.

In the final stage of the research, we are developing new methods for inferring retrovirus expression from databases. The methods will be general-purpose in the sense that they should be applicable to disambiguating cross-talk in other kinds of expression studies as well.

Selected publications:

Oja M., Göran O. Sperber, Jonas Blomberg, and Samuel Kaski. Self-organizing map-based discovery and visualization of human endogenous retroviral sequence groups. International Journal of Neural Systems, 15(3):163–179. 2005.

Hu L, Hornung D, Kurek R, Östman H, Blomberg J, Bergqvist A. Expression of Human Endogenous Retroviruses in Endometriosis and Ovarian Cancer. Accepted, AIDS Research and Human Retroviruses (2006).

Muradrasoli S, Forsman A, Hu L, Blikstad V, Blomberg J. Development of Real-Time PCRs for Detection and Quantitation of Human MMTV-like (HML) sequences. HML expression in human tissues and cell lines.  Accepted with revision, J Virol Meth (2006).

An abstract of the research plan (January 2003)