Samuel Andersson
Bioinformatic Exploration of Antisense Transcripts

Master Thesis in Bioinformatics

Advisors: Jari Häkkinen and Markus Ringnér

Abstract:
Scientists are using microarrays to experimentally measure the expression levels of many individual genes simultaneously. cDNA microarray assays use DNA base-pairing to indirectly measure sequence specific mRNA concentrations, which are believed to reflect gene expression levels. There have been indications that antisense mRNA are more common than expected and it is interesting, and important, to understand how antisense mRNA affects the result of measurements. The aim of this project was two folded; i) to build a software package which create a dynamic database of array clone information (ACID) consisting of complete information of clones used in microarray experiments, and ii) writing an application to find which clones are part of antisense mRNA. Identifying these clones is a first step for further studies of the effect from antisense mRNA.

Most of the information in ACID is collected from well known databases such as UniGene and GenBank. 2368 identified antisense mRNA sequences corresponding to 3032 clones have been found sofar . The list cannot be seen as final before it is known which clones really are located in the overlapping sense-antisense regions of the mRNA sequences.

LU TP 03-26, June 2003