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Table 3 Gene ontology enrichment analysis

From: The antineoplastic drug, trastuzumab, dysregulates metabolism in iPSC-derived cardiomyocytes

 

Small molecule metabolic process (GO:0044281)

Cholesterol metabolic process (GO:0008203)

Sterol metabolic process (GO:0016125)

Cholesterol biosynthetic process (GO:0006695)

Sterol biosynthetic process (GO:0016126)

iPSC cardiomycytes treated with trastuzumab

 Genes uploaded to enrichment analysis

428/517

428/517

428/517

428/517

428/517

 Uploaded genes in category

98

12

NS

8

8

 Expected genes in category

45.92

2.24

0.78

0.88

 Category fold enrichment

2.13

>5

>5

>5

 p value (adjusted)

3.22E−09

0.030

0.013

0.031

iPSC cardiomycoytes treated with lapatinib

 Genes uploaded to enrichment analysis

1077/1358

1077/1358

1077/1358

1077/1358

1077/1358

 Uploaded genes in category

173

21

21

12

12

 Expected genes in category

115.54

5.64

6.31

1.97

2.22

 Category fold enrichment

1.5

3.72

3.33

>5

>5

 p value (adjusted)

4.94E−04

0.004

0.022

0.009

0.030

ERBB2-overexpressing cancer cell lines treated with trastuzumab

 Genes uploaded to enrichment analysis

2097/2272

2097/2272

2097/2272

2097/2272

2097/2272

 Uploaded genes in category

340

32

32

22

22

 Expected genes in category

224.97

10.98

12.29

3.83

4.33

 Category fold enrichment

1.51

2.91

2.6

>5

>5

 p value (adjusted)

1.23E−10

0.001

0.014

1.12E−06

1.06E−05

  1. Differentially expressed genes following treatment with trastuzumab or lapatinib were assessed for enrichment in gene ontology categories of biological process. 517 genes were significantly differentially expressed in iPSC-derived cardiomyocytes following treatment with trastuzumab. 428/517 genes were recognized within the Gene Ontology (GO) Consortium reference dataset of 20,814 genes and analyzed for enrichment. Similarly, of 1358 differentially expressed genes following treatment of iPSC-derived cardiomyocytes with lapatinib, 1077 were recognized in the GO reference set and analyzed for enrichment. Of 2272 differentially expressed genes following treatment with trastuzumab in ERBB2-overexpressing cancer cell lines, 2097 were recognized in the GO reference set and analyzed for enrichment. Enrichment analyses showed 1.5- >5-fold enrichment of genes in cholesterol processing pathways relative to expected, based on the annotated reference set of 20,814 genes