Discussion:The basic statistics in Figures 1.1 and 1.2 show that noreads were flagged for poor quality. This combined with the good per basesequence quality with low decrease in quality in the 3′ end of the read andsequence quality score over 20 (with peak at 30) indicate that the RNA-seqreads are of reasonable quality. Additionally, the quality of the reads betweendatasets is very similar, meaning they are comparable.In figure.
3 , most exons of the brain data mapping to thelong arm of chromosome 5 shows strong association between chromosome 5 andgenes to do with regulating brain function. The lack of many introns and densepacking of exons suggests that large regions of chromosome 5 are non-coding.Table 1 shows that the gene most over expressed in the braincompared to the heart is janus kinase and microtubule interacting protein 2(JAKMIP2), a gene that likely encodes for proteins that are components of theGolgi matrix.
It is likely that this protein is involved in secretary transportthrough downregulating. Approximately the same amount of genes are overexpressed in the brain compared to the heart as are under expressed. This couldindicate that In figure 10, the proteins that have the best conservationacross species in relation to Homo sapiens are the mouse, rat and chimpanzee.This suggested that they are phylogenetically the closest as their genomesequence would have diverged later than that of Homo sapiens and the otherorganisms shown.The reasons why figures 11.1 and 11.2 differ are as follows:In figure 11.
1 the species that Homo sapiens last divergedfrom was the chimpanzee, second was the dog. The maximum parsimony tree choosesthe route with the fewest changes in the gene code. This method is slow tocarry out, especially on larger datasets and requires a large amount ofcomputational effort. This method can also be seen as over simplistic and lesslikely to provide an accurate tree. In figure 11.2 the minimum evolution model is applied, whichis somewhat based on the same idea as the maximum parsimony trees. The programcomputes the distance based on how far all of the pairs are away from eachother and constructs branch length on this basis. This is repeated for allpossible variations of the tree and the one with the smallest overall distancesis selected.
This method requires less computational energy than the MP, butstill 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 aheuristic algorithm. (Nei, 19874) In figure 11.4, theBootstrap method was applied. This helps to add measures of statisticalsignificance to the branches. It adds numbers that show measures of confidencein graphs. For example you can see that figure 11.5 has 83 next to the Homosapiens branch as opposed to 81 in figure 11.4.
It can be concluded that the Neighbour joining tree incombination with the bootstrap method at a level 100 is the best system to usewhen creating phylogenetic trees in this instance. Conclusion:Differential gene expression between the heart and the lungsof genes on chromosome 5 of Homo sapiens is very prominent. Most of the exonsin the genes for the heart and lungs map to a small region on the long arm ofchromosome 5 with large non-coding areas surrounding.
