Gene expression variation in Downs syndrome mice allows prioritization on candidate genes' Marc Sult

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Gene expression variation in Downs syndrome mice
allows prioritization on candidate genes.Marc
Sultan, Ilaria Picini, Daniela Balsereit, Ralf
Herwig, Nidhi G Saran, Hans Lehrach, Roger H
Reeves and Marie_laure Yaspo
BACKGROUND
RESULTS - Continued
FIGURE 1 Differentially Expressed Genes
Down Syndrome or Trisomy 21 is characterized by
an extra copy of chromosome 21 (Hsa 21) as seen
in the image at left. This study focuses on the
cognitive impairments caused by this extra
allele. Specifically fifty mmu21 genes were
selected as ones of interest from previous
studies. These genes are located in the
midbrain, cortex, and cerebellum regions of the
brain. Samples were taken from eight Ts65Dn mice
(diseased) and eight control mice called euploids
or litter mates. Because there is a biological
log-fold
The second group are genes whose Wilcoxon
p-values were between 0.01 and 0.05. These genes
might be considered as a variable part of the
phenotype (i.e. in some individuals it may be
important to consider these). The last group
consists of those genes whose p-values were
greater than 0.05 and should probably be ruled
out as having a significant effect on Downs
Syndrome. It is interesting to note that the
authors looked at the gene ontology of the gene
App which shows up with highly significant
p-values in each of the three tissue areas of the
brain. The authors point out that this gene is
known to mutate in some forms of Alzheimers
disease and when up-regulated in involved in the
degeneration of cholinergic neurons. (Salehi et.
al)
Image of trisomy 21. The 3rd chromo-some noted
by the arrow is the cause of Downs Syndrome.
Science Source/Photo Researchers, Inc.
change of 1.5 in pooled treatment vs. control
studies due to this extra copy of Hsa 21 it is
difficult to determine which genes are
differentially expressed. This paper discusses
the value of looking at individual expression
values when the data is not pooled and offers
ideas into the interpretation of these values in
selecting candidate genes.
DISCUSSION
RT-PCR seems to be an interesting alternative to
micro-array technology. Both are based on
measuring the amount of mRNA resulting from a
biological process. I would be interested to see
a comparison between the two methods. (e.g. 6820
project). There seems to be subjectivity based
on the genes you choose in RT-PCR. This limits
your scope based on past experiments, where
micro-array technology will give you a look at
tens of thousands of genes and then it can be
determined if there are any relationships.
Also the paper mentioned that normalization was
based on a small set of non-differentially
expressed genes. It seems stronger to do
quantile normalization based on the whole array.
One of the strengths of the methods chosen by
the authors is the ability to look at each gene
individually. Although there is proven to be a
large amount of inter-individual variation it is
interesting to see for which genes this variation
occurs. This is similar to looking at the
coefficient of variation on the
micro-arrays. The coefficient of variability
also is discussed by the authors as a determining
factor in gene selection, not just because that
is where the information is, but because a second
tier of genes that sometimes express themselves
highly should still be considered genes of
interest.
METHODS
Because pooling of the treatment and control
groups results in the overall log fold change of
1.5, the authors chose to look at individual
differences in expression values between genes
from the diseased mouse and its littermate. The
ratios of these values were then considered based
on their mean log fold change and their
variability. The authors chose to quantify
expression levels using Real-Time quantitative
polymerase chain reaction. This is a chemical
method used to measure the amount of mRNA that is
a result of a genetic bonding. In essence the
gene probes of interested are fluoresced and
placed in a chemical solution with the reagent.
The chemical solution it is placed in initially
prevents the detection of the fluorescent. The
process of polymerase chain reaction releases the
luminescent and its chemical suppressant and
light intensities increase. The intensities are
measure over time and compared to values measured
from the control group to quantify expression
levels. Tests for differential expression can
then be conducted based on the group of genes
used in the chemical solutions.
RESULTS
The above genes are grouped in three categories,
according to P value resulting from the Wilcoxon
test and the part of the brain from which they
were tested. The first category (left) shows
genes with P lt 0.01, meaning that the expression
levels in Ts65Dn individual mice are consistently
different from euploids. The second category
shows genes with 0.01 ltP lt 0.05, for which the
expression levels of Ts65Dn samples partially
overlap with euploids. The last category (P gt
0.05) groups genes for which the expression
levels between Ts65Dn and euploid mice cannot be
distinguished. Genes in the first category might
be responsible for the fully penetrant signs in
trisomy, genes in the second could contribute to
the variable signs, whereas the third category
contains genes that may make little or no
contribution. - Graph and legend attributed to
the authors (Sultan, et. al)-
References
The authors classified the original 50 genes
into three different groups based on the p-value
resulting from the Wilcoxon Rank Sum Test. This
grouping is shown in figure 1. Group one
contains genes whose p-value was less than 0.01.
This group represents genes for which there was a
high level of separation between the expression
level of any member of the treatment group and
any other euploid. These genes could be
considered good candidates that should be
included in the phenotype of Downs Syndrome.
Sultan, et al Gene expression variation in Downs
syndrome mice allows prioritization of candidate
genes. Genome Biology 2007, 8R91 Salehi, A et al
Increased App expression in a mouse model of
Downs syndrome disrupts NGF transport and cause
cholinergic neuron degeneration. Nueron 2006,
5129-42 Dharamaj, Subbu RT-PCR The Basics
Applied Biosystems http//www.ambion.com/techlib/b
asics/rtpcr/index.html