Results

Below are the results of the figure reproductions and bioinformatics analyses:

Table 1

Data Visualization Testing

Test Figure Expected figure Reproduced figure Degree

case # being of
reproduced similarity
(1-5)

1 1e 3
2 2c 3
 3 2a 4

Table 2

Bioinformatics Analysis Testing

Test case # Associated Analysis of the Analysis of the Conclusion

figure associated figure reproduced
figure

1 1e A large number Low numbers of H3K9me3 is a

of H3K9me3 stage specific repressive
established genes are marker, thus the
marks are shown expressed in 4 higher the
on the 4 cell, 8 cell, 8 cell, and number of
cell, and morula morula stages. established
stages. H3K9me3
marks, the lower
the number of
genes specific to
stages.
Satisfactory
match.
2 2c The P values in The P values in The reproduced
the figure range most of the figures' P values
from 5 to 10. tables range for GO terms do
from 1 to 8. not match the
 Only in 2 cell, 4 range of P
cell, and 8 cell values for the
downregulated expected graph,
GO analysis do indicating
the P values go different
above 10. biological
processes to be
significant.
Unsatisfactory
match.
3 2a Normalized Weaker gene Strong
H3K9me3 input expression in 2 H3K9me3 marks
ratio is high in cell and 4 cell in the ChIP-seq
MII, zygote, 2 stages. original is met
cell, and 4 cell with weak
stages. specific gene
expression in the
next stage in the
RNA-seq
reproduction.
Both
complement
each other.
Satisfactory
match.

Regarding the reproductions of the figures, the reproduction of figure 1e had a degree of

similarity of 3, indicating that a data limitation prevented a visually identical reproduction. The

gene ontology tables, which were the reproduction of figure 2c from the paper by Wang et al.

(2018), has a degree of similarity of 3 as well, also indicating that a data limitation prevented a

visually identical reproduction. The reproduction of figure 2a had a degree of similarity of 4.

The bioinformatics analysis reproduction results indicate that the data for both the

reproduction and the associated figure contain the same conclusion for figure 1e, making the

reproduction a satisfactory match. However, the reproductions of figure 2c contained P values

that are different in ranges compared to the associated figure, leading to a conclusion of an
unsatisfactory match of bioinformatics analyses. The reproduction of figure 2a showed a mostly

light blue to dark blue color in terms of gene expression in the 2 cell and 4 cell stages, which

indicated weaker gene expression in these stages.

Evaluation of Findings

Although the figure reproductions were not visually identical to the original figures and

therefore neither are some of the bioinformatics analyses of the reproductions, these differences

were expected due to a difference in the type of data the researcher and Wang et al. (2018) used.

Wang et al. (2018) used ChIP-seq data, which measures H3K9me3 marks, whereas the

researcher uses RNA-seq data. In the context of biology, the results of the reproductions, while

they initially seemed contradictory compared to the figures, are complementary. H3K9me3 is a

repressive marker which stops genes from being expressed. The higher the concentration of

H3K9me3 marks, the fewer the number of genes that are expressed. Comparing figure 1e to the

RNA-seq reproduction visualization with this knowledge explains why the bioinformatics

analysis of the two lead to the same conclusion: the reproduction showed a lower number of

genes specific to a stage being expressed at points where there are many H3K9me3 marks. The

mismatch in gene ontology tables was also expected, as gene ontology analysis for H3K9me3

marks is bound to be different compared to genes specific to embryonic stages. In fact, due to the

difference between ChIP-seq and RNA-seq data, the gene ontology tables were expected to not

match. The heat maps were expected to match, and thus they reached the same conclusion based

off of the information.

Summary

Without any knowledge of genetics, the figures and bioinformatics analysis compared to

their RNA-seq reproductions may seem to portray contradictory data due to a lack of visual
similarity. However, with knowledge of how H3K9me3 affects gene expression and knowledge

of the difference between RNA-seq and ChIP-seq data, the original figures and bioinformatics

analysis were complementary with their RNA-seq reproduction counterparts, as some data is

meant to be similar, while other data is not.