Paterson Institute for Cancer Research SCIENTIFIC REPORT 2005

BIOINFORMATICS
age, MIAME VICE is becoming the main route of
data exchange between the Molecular Biology Core
Facility (page 52) and its users.
The complex relationship between genes,
probes and transcripts
Affymetrix microarrays record the presence of a
transcript in solution by measuring the level of
hybridization between the transcript and a set of
short (typically 25mer) oligonucleotide probes
anchored to the array surface. Each ‘probe-set’
consists of a series of ‘perfect match’ (PM) probes,
designed to match exactly to the transcript, and a
series of ‘mismatch probes’ (MM), identical to the
PM probes except that the middle residue has been
changed. Hybridization conditions are controlled
with the aim of maximizing the binding between a
transcript and its PM probes, whilst minimizing the
binding to its MM probes (see www.affymetrix.com
for more details). The intention is that the PM
probes record the presence of the transcript, whilst
MM probes measure background and non-specific
hybridization. One advantage of this approach is
that the combination of short oligonucleotides and
strict hybridization conditions makes it possible to
use in silico searches to predict which probes are likely
to bind to which transcripts; information that is
important because many transcripts have similar
sequences and certain probes are capable of binding
to more than one mRNA molecule (for example
because alternate splicing can lead to a set of
transcripts being encoded by a single gene; due to
homology; or due to repetitive or low complexity
regions).
Not only do some probesets target multiple transcripts,
the reverse is also true – there are multiple
probesets that target a single transcript. This can
occur, for example, with probe-sets designed to
identify different splice-variants of the same gene,
or where one probeset is designed to identify a gene
family, whilst another targets a particular family
member (see figure).
Identifying these situations is useful when considering
experimental data in which evidence from a particular
probeset is weak. If all the other probesets
targeting the same transcript behave similarly, this
can provide supporting evidence; if they behave
differently it may be possible to discount the probeset
from further analysis. We have developed an
online database, ADAPT, that allows these complex
relationships to be investigated.
Comparisons between protein and mRNA gene
expression data
A significant opportunity exists to place proteomics
and microarray data side by side, allowing comparison
of changes in gene expression at the transcript
and protein level. To do this requires complex
mappings to be made between genomic, transcript
and protein sequences; a difficult task because of
the structure of existing databases and the complex
many-many relationship that exists between genes
and gene products. We have been developing software
tools and analysis strategies to support these
analyses in collaboration with Professor Tony
Whetton at the University of Manchester and the
Kouskoff and Lacaud groups at the Paterson
Institute.
The complex many-many relationships that exist between
Affymetrix probesets (blue balls) and transcripts (yellow balls)
for the HGU133 array.
P A T E R S O N I N S T I T U T E S C I E N T I F I C R E P O R T 2 0 0 5
Publications listed
on page 56
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