Freshwater Clam Extract Ameliorates Triglyceride and Cholesterol Metabolism through the Expression of Genes Involved in Hepatic Lipogenesis and Cholesterol Degradation in Rats

Table 3

Various biofunctions and pathways were altered in the rat liver by the FCE diet compared with control.

Category	P value	Gene	Upregulated genes	Downregulated genes
Biofunctions^a
Lipid metabolism	1.55𝐸−13	83	42	41
Small molecule biochemistry	1.55𝐸−13	103	55	48
Vitamin and mineral metabolism	9.80𝐸−13	34	18	16
Drug metabolism	2.88𝐸−10	26	21	5
Molecular transport	5.96𝐸−07	64	34	30
Nucleic acid metabolism	1.29𝐸−06	16	6	10
Carbohydrate metabolism	1.55𝐸−04	39	17	22
Cell death	1.57𝐸−04	21	19	2
Amino acid metabolism	7.70𝐸−04	17	15	2
Cell cycle	1.21𝐸−03	10	7	3
Cellular assembly and organization	1.21𝐸−03	9	2	7
Gene expression	1.21𝐸−03	15	11	4
Cellular function and maintenance	1.31𝐸−03	7	6	1
Cellular compromise	3.54𝐸−03	9	6	3
Cellular growth and proliferation	4.16𝐸−03	4	3	1
Cell-to-cell signaling and interaction	6.91𝐸−03	7	4	3
KEGG pathways^b
Polyunsaturated fatty acid biosynthesis	5.95𝐸−06	7	0	7
Metabolism of xenobiotics by cytochrome P450	7.81𝐸−06	12	12	0
Biosynthesis of steroids	8.09𝐸−05	7	0	7
C21-steroid hormone metabolism	2.79𝐸−04	5	3	2
Androgen and estrogen metabolism	3.08𝐸−04	9	6	3
PPAR signaling pathway	1.92𝐸−03	9	1	8
Linoleic acid metabolism	3.14𝐸−03	6	6	0
Alanine and aspartate metabolism	3.61𝐸−03	6	3	3
Maturity onset diabetes of the young	7.55𝐸−03	5	0	5
Pyruvate metabolism	1.03𝐸−02	6	1	4
Bile acid biosynthesis	2.68𝐸−02	5	4	1
Glutathione metabolism	3.48𝐸−02	5	4	1
Carbon fixation	3.56𝐸−02	4	1	3
Nitrogen metabolism	3.56𝐸−02	4	2	2

We compared the effect of the FCE diet on hepatic gene expression with that of control by using oligonucleotide microarray.
^aDifferentially expressed gens list from microarray experiment was imported in Ingenuity pathway analysis, filtered by selecting only genes expressed in rat liver. Significance values expressed as P values were calculated using a right-tailed Fisher's exact test. Biofunctions that were significantly changed were determined.
^bWe conducted KEGG pathway analysis by importing a list of differentially expressed genes in DAVID (database for annotation, visualization, and integrated discovery). Significance values expressed as P values were calculated using a modified Fisher exact probability test (EASE score).