CLASSIFICATION OF CHEMICAL COMPOUNDS BASED ON THE CORRELATION BETWEEN IN VITRO GENE EXPRESSION PROFILES

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Received: March 3, 2021

Revised: May 13, 2021

Accept: May 21, 2021

Classification of compounds based on in vitro gene expression profiles

Dissimilality measures

Figures

The nine chemicals in duplicate

Figure 1: A dendrogram obtained by applying aggregative hierarchical clustering (the

average linkage between the merged groups) to the data of the gene expression ratios

for the nine compounds and 32,586 RNAs. The y-axis marks the dissimilarity measures

at which the clusters merge, and the x-axis the distribution of the nine compounds in

duplicate.

J. Takeshita, A. Toyoda,H. Tani, Y. Endo, and S. Miyamoto

Dissimilality measures

10

The nine chemicals in duplicate

Figure 2: A dendrogram obtained by applying aggregative hierarchical clustering (the

average linkage between the merged groups) to the data of the gene expression levels

for the nine compounds and 32,586 RNAs. The y-axis marks the dissimilarity measures

at which the clusters merge, and the x-axis the distribution of the nine compounds in

duplicate.

11

Dissimilarity measures

Dissimilarity measures

Classification of compounds based on in vitro gene expression profiles

The nine compounds in duplicate

(a) α = 0.0

(b) α = 0.1

Dissimilarity measures

Dissimilarity measures

The nine compounds in duplicate

The nine compounds in duplicate

The nine compounds in duplicate

(c) α = 0.2

(d) α = 0.3

Figure 3: Four dendrograms obtained by applying aggregative hierarchical clustering

(the average linkage between the merged groups) to the data of the gene expression

ratios for the nine compounds and 3, 000 extracted RNAs. The upper-left (a), upperright (b), lower-left (c) and lower-right (d) panels are the cases of α = 0.0, 0.1, 0.2, and

0.3, respectively. In each panel, the y-axis marks the dissimilarity measures at which

the clusters merge, and the x-axis the distribution of the nine compounds in duplicate.

Dissimilarity measures

J. Takeshita, A. Toyoda,H. Tani, Y. Endo, and S. Miyamoto

Dissimilarity measures

12

The nine compounds in duplicate

(a) α = 0.0

(b) α = 0.1

Dissimilarity measures

Dissimilarity measures

The nine compounds in duplicate

The nine compounds in duplicate

The nine compounds in duplicate

(c) α = 0.2

(d) α = 0.3

Figure 4: Four dendrograms obtained by applying aggregative hierarchical clustering

(the average linkage between the merged groups) to the data of the gene expression

ratios for the nine compounds and 1, 000 extracted RNAs. The upper-left (a), upperright (b), lower-left (c) and lower-right (d) panels are the cases of α = 0.0, 0.1, 0.2, and

0.3, respectively. In each panel, the y-axis marks the dissimilarity measures at which

the clusters merge, and the x-axis the distribution of the nine compounds in duplicate.

13

Dissimilarity measures

Dissimilarity measures

Classification of compounds based on in vitro gene expression profiles

The nine compounds in duplicate

(a) α = 0.0

(b) α = 0.1

Dissimilarity measures

Dissimilarity measures

The nine compounds in duplicate

The nine compounds in duplicate

The nine compounds in duplicate

(c) α = 0.2

(d) α = 0.3

Figure 5: Four dendrograms obtained by applying aggregative hierarchical clustering

(the average linkage between the merged groups) to the data of the gene expression

ratios for the nine compounds and 100 extracted RNAs. The upper-left (a), upper-right

(b), lower-left (c) and lower-right (d) panels are the cases of α = 0.0, 0.1, 0.2, and 0.3,

respectively. In each panel, the y-axis marks the dissimilarity measures at which the

clusters merge, and the x-axis the distribution of the nine compounds in duplicate.

14

J. Takeshita, A. Toyoda,H. Tani, Y. Endo, and S. Miyamoto

Figure 6: Scatter plot of all the RNAs (32, 586 RNAs) between the sample 1 and 2

in case of bis-phthalate. The red plots indicate the 1, 000 extracted RNAs in case of

α = 0.0, and the blue plots are the rest RNAs. The sizes of the extracted RNAs are

almost zeros.

Figure 7: Scatter plot of all the RNAs (32, 586 RNAs) between the sample 1 and 2

in case of bis-phthalate. The red plots indicate the 1, 000 extracted RNAs in case of

α = 0.2, and the blue plots are the rest RNAs. The number of RNAs whose sizes are

not zeros increase, compared to the case of α = 0.0.

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