Microarray bioinformatics at DNR/UiO

Ongoing projects:

• Storage, normalization and filtering of microarrays: BASE development. This is presently the main tool for microarray users looking for help.
• Evaluation of amplification protocols, experiment design
• Genomic arrray tools development
• Microarray analysis
• Infrastructure development

Are you a microarray user in the Oslo region looking for some support in this complex area?We offer some help in these matters, assisting you in using BASE:

1. First line support for users trying to figure out how and when to store data: Nina Kristiansen. She will also help in transferring clone information from the slides to your local scanner, if you have this need.
2. First line support for users trying to do basic BASE work to normalize and filter their own data: Signe Indahl or Nina Kristiansen (microarray user support for UiO) .
3. Second line support for users desperately stuck using BASE, having tried all options, consulted Signe, and read all available docs: Vegard Nygaard.
4. All other requests regarding new bioinformatics questions of microarrays may be adressed to Eivind Hovig. (+47-22935416).

Personnel at various levels and areas of expertise:

• Nina Kristiansen
• Fang Liu
• Vegard Nygaard
• Tor-Kristian Jenssen
• Eivind Tøstesen
• Eivind Hovig

Collaborators

• Norwegian Computing Center
• PubGene

Microarray related bionformatics papers from the Norwegian Radium Hospital

• Quality control: Repeatability analysis
• Tool for handling small number of experiments, such as forward and reverse labelling:MArray
• Litterature analysis for microarrays: PubGene tools described in this paper
• Downstream analysis: Survival analysis of microarrays
• Clustering of microarray data using SOM.