A link between multiple high throughput technology datasets

Elmar Bucher, Pekka Kohonen, Vidal Fey, John Mpindi, Henri Sara, Tommi Pisto, Henrik Edgren, Sami Kilpinen, Kalle Ojala, Pekka Tiikkainen, Paula Vainio, Kristiina Iljin, Niko Sahlberg, Juha K. Rantala, Rami Mäkelä, Petri Saviranta, Merja Perälä, Matthias Nees, Saija Haapa-Paananen, Olli Kallioniemi

Research output: Chapter in Book/Report/Conference proceedingConference abstract in proceedingsScientific

Abstract

Our laboratory performs high-throughput screening (HTS) experiments using siRNA, miRNA and compound libraries on cancer-cell lines. We utilize three technologies: plate-based screens with different assays as endpoints, transfected cell arrays with up to four antibody endpoints, and protein lysate arrays allowing many immunostaining endpoints. In addition, we profile samples using at least three commercially available microarray technologies: gene expression using Affymetrix arrays, miRNA expression using Agilent arrays, and gene copy numbers (aCGH) using Agilent arrays. This enables us to study the same biological sample from multiple angles which provides a unique integrated opportunity to understand cancer. The database design presented here is based on the idea that different high-throughput technologies can be integrated at the gene level.
Original languageEnglish
Title of host publicationThe 9th International Conference on Systems Biology (ICSB2008)
Subtitle of host publicationAbstract book
Pages186
Publication statusPublished - 2008
Event9th International Conference on Systems Biology, ICSB2008 - Göteborg, Sweden
Duration: 22 Aug 200828 Aug 2008

Conference

Conference9th International Conference on Systems Biology, ICSB2008
Abbreviated titleICSB2008
CountrySweden
CityGöteborg
Period22/08/0828/08/08

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Keywords

  • high througput screening technology
  • database design
  • database management system
  • R
  • MySQL

Cite this

Bucher, E., Kohonen, P., Fey, V., Mpindi, J., Sara, H., Pisto, T., Edgren, H., Kilpinen, S., Ojala, K., Tiikkainen, P., Vainio, P., Iljin, K., Sahlberg, N., Rantala, J. K., Mäkelä, R., Saviranta, P., Perälä, M., Nees, M., Haapa-Paananen, S., & Kallioniemi, O. (2008). A link between multiple high throughput technology datasets. In The 9th International Conference on Systems Biology (ICSB2008): Abstract book (pp. 186)