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BDSP: Analyzing the evolution of PSI profiles using Principal an
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Component Analysis
Carmen Le, Carina Kalaydjian, Claire Mayfield, Miguel Guardado, Alia Edington,
Jeanice Nyung, Rori Rohlfs

Background Results Conclusions

● Our results suggest that mice are not as closely related to humans,
Blue -> Chimpanzees chimpanzees, and macaques as they are to each other due to the
Red -> Humans great distance between the mice and other species on each plot.
Green -> Macaques ● We also believe that there is a strong relation between chimpanzees
Purple -> Mice and humans based on the close clumping patterns in all of the PCA
plots.
● We believe that the divergence seen in the PVC and the cerebellum
LIPIDS Cerebellum LIPID PVC (Primary Visual Cortex) analysis between primates and mice is due to the differences in
location of the eyes on the head and because mice are quadrupeds.
● We believe that the divergence seen in the PVC and the cerebellum
analysis between apes and old world monkeys such as macaques
Pro Promet Met Ana Telo
could be due to difference in daily activities that require amplified
depth perception and balance.C
Figure 1. Schematic of Alternative Splicing
Genetic information is the template for formation of functional products called
proteins. An essential component of this process is translation, which uses three
ribonucleic acid (RNA) nucleotides , called codons, where each codon corresponds to
a specific amino acid. The connected amino acids then form a protein. The initial RNA
(pre-mRNA) strand will have two parts; non-coding regions (introns) and coding
LIPID Kidney Kaessmann Heart
regions (exons). Before constructing the protein, RNA must be primed with only exons
through a mechanism called splicing. During splicing, a protein complex called the
spliceosome will excise the introns; therefore, leaving the new mature RNA (mRNA)
ready for translation. Another way of excising exons is through a process called
alternative splicing, which will rearrange the exons in different order to form different
proteins. Our project involved examining the degree to which various exons are
included in mature RNA transcripts, better known as Percent Spliced In (PSI) values Figure 4. This phylogenetic tree was produced to explain the evolutionary
in four species. relationship between mice, macaques, chimpanzees, and humans.
T –T
This tree also supports our findings that humans and chimps share a more recent
common ancestor than they do with macaques or mice.

LIPID PFC(Prefrontal Cortex)

Future Directions
● Further analyze Lipid and Kaessmann
datasets using the Expression
Variance and Evolution (EVE) model,
a program that tests for divergence
and diversity in exon expression
Figure 2. Schematic of Principal Component Analysis (PCA). levels using phylogenetic data.
Additionally, this model shows

PC2
PCA is the statistical process of reducing the dimensions of large datasets into smaller expression evolution within and
datasets to help get a better picture of what the overall data set looks like. We achieve between different species (Rohlfs,
this by getting the principal components of the data by use of the dataset’s orthogonal Figure 3. PCA plots of various tissues from Lipid and Kaessman datasets. Each 2018).
transformation. Using this statistical procedure for looking at PSI values inside exons plot is from one of five tissues with four species. The number of individuals ● Analyze exon clusters found in
can help take the large data of values and help cluster them together. This will highlight from each species is dependent on the data set and tissue. previous PCA performed on individual
what types of species and tissues will be closely related to each other. Analyzed by exons (left). Black represents
tissue, we can then predict that the closer the species clustering is to each other the In each figure, mice are clustered together and are further away from the other three individual exons by number and the
more closely related each individual species are to one another. (Prakhar, 2018) species: humans, chimpanzees, and macaques. Each species has a unique red arrows represent the diverging
clustering pattern in each tissue, but there is a trend where all the individuals within species.
each species remain clustered together. An exception for this is in the Kaessmen PC1

Hypothesis heart plot where HUM1 appears to be an outlier. When looking at the plots that
represent different lobes of the brain, there are significant clustering among primates.
In the Cerebellum, PVC, and PFC, the humans and chimpanzees are closely References
Percent spliced in (PSI) values identify the frequency at which a particular clustered together and, at some points, overlap one another. The old world monkey,
the macaque, is not closely clustered to the other primates; therefore, suggesting that 1. Mishra, Prakhar. 2018. “A Layman’s Introduction to Principal Components – Hacker
exon is present in the mature RNA transcript in a specific tissue. We
Noon.” Hackernoon. 2018.
hypothesize that the PSI profiles for humans, chimps, and macaques human and chimpanzees have more similar splicing patterns than macaques do
https://hackernoon.com/a-laymans-introduction-to-principal-components-2fca55c19f
will have higher similarities to each other than to mice. within primates.
a0.
2. Rohlfs, Rori V., and Rasmus Nielsen. “Phylogenetic ANOVA: The Expression
Variance and Evolution Model for Quantitative Trait Evolution.” Systematic Biology
64.5 (2015): 695–708. PMC. Web. 24 July 2018.