The basic statistics in Figures 1.1 and 1.2 show that no
reads were flagged for poor quality. This combined with the good per base
sequence quality with low decrease in quality in the 3′ end of the read and
sequence quality score over 20 (with peak at 30) indicate that the RNA-seq
reads are of reasonable quality. Additionally, the quality of the reads between
datasets is very similar, meaning they are comparable.
In figure.3 , most exons of the brain data mapping to the
long arm of chromosome 5 shows strong association between chromosome 5 and
genes to do with regulating brain function. The lack of many introns and dense
packing of exons suggests that large regions of chromosome 5 are non-coding.
Table 1 shows that the gene most over expressed in the brain
compared to the heart is janus kinase and microtubule interacting protein 2
(JAKMIP2), a gene that likely encodes for proteins that are components of the
Golgi matrix. It is likely that this protein is involved in secretary transport
through downregulating. Approximately the same amount of genes are over
expressed in the brain compared to the heart as are under expressed. This could
In figure 10, the proteins that have the best conservation
across species in relation to Homo sapiens are the mouse, rat and chimpanzee.
This suggested that they are phylogenetically the closest as their genome
sequence would have diverged later than that of Homo sapiens and the other
The reasons why figures 11.1 and 11.2 differ are as follows:
In figure 11.1 the species that Homo sapiens last diverged
from was the chimpanzee, second was the dog. The maximum parsimony tree chooses
the route with the fewest changes in the gene code. This method is slow to
carry out, especially on larger datasets and requires a large amount of
computational effort. This method can also be seen as over simplistic and less
likely to provide an accurate tree.
In figure 11.2 the minimum evolution model is applied, which
is somewhat based on the same idea as the maximum parsimony trees. The program
computes the distance based on how far all of the pairs are away from each
other and constructs branch length on this basis. This is repeated for all
possible variations of the tree and the one with the smallest overall distances
is selected. This method requires less computational energy than the MP, but
still needs a lot.
Figure 11.3 was produced by another distance based method,
the Neighbour Joining tree. This tree minimises branch length in stages using a
heuristic algorithm. (Nei, 19874) In figure 11.4, the
Bootstrap method was applied. This helps to add measures of statistical
significance to the branches. It adds numbers that show measures of confidence
in graphs. For example you can see that figure 11.5 has 83 next to the Homo
sapiens branch as opposed to 81 in figure 11.4.
It can be concluded that the Neighbour joining tree in
combination with the bootstrap method at a level 100 is the best system to use
when creating phylogenetic trees in this instance.
Differential gene expression between the heart and the lungs
of genes on chromosome 5 of Homo sapiens is very prominent. Most of the exons
in the genes for the heart and lungs map to a small region on the long arm of
chromosome 5 with large non-coding areas surrounding.