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
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