Table 1.

Summary of fish species, analyzed organ, sampling time point, transcriptome analysis method, and the number of up- and downregulated DEGs of the eligible publications analyzed in the present review. N/A: non applicable.

Fish Species	Organ Sample/Cell Culture	Sampling Time	Analysis Method	Number of Up-Regulated DEGs	Number of Down-Regulated DEGs	Reference
Psetta maxima	Head kidney	3 hpi; 6 hpi; 24 hpi; 3 dpi	Microarray	94	12	[29]
Epinephelus spp.	Grouper kidney cells	6 hpi; 33 hpi	RNA-Seq	N/A	N/A	[30]
Epinephelus coiodes	Larvae whole	natural infection	Microarray	17	47	[31]
Gadus morhua	Brain	5 dpi; 11 dpi; 25 dpi	Microarray	1179	454	[32]
Oryzias latipes	Whole fish	24 hpi	Microarray	N/A	N/A	[33]
Danio rerio	Embryonic-derived zebrafish cells	6 hpi	Microarray	N/A	N/A	[34]
Lates calcarifer	Epithelial cells	6 hpi; 12 hpi; 24 hpi; 48 hpi	RNA-Seq	N/A	N/A	[35]
Channa striatus	Striped snakehead fish cells	3 hpi; 24 hpi	RNA-Seq	1184, 3 hpi 1138 24 hpi	1456, 3 hpi 2073, 24 hpi	[36]
Dicentrarchus labrax	Head-kidney leucocytes	4 hpi	RNA-Seq	N/A	N/A	[37]
Hyporthodus septemfasciatus	Brain	3 dpi; 4 dpi	RNA-Seq	N/A	N/A	[38]
Epinephelus coiodes	Grouper fin cell line	3 hpi; 24 hpi	RNA-Seq	43	8	[39]
Lateolabrax japonicus	Lateolabrax japonicus brain cells	48 hpi	RNA-Seq	1969	9858	[40]
Solea senegalensis	Head kidney; eye/Brain	48 hpi	RNA-Seq	N/A	N/A	[41]
Epinephelus malabaricus	Brain	9 dpi	RNA-Seq	N/A	N/A	[42]
Dicentrarchus labra	D. labrax brain cells	12 hpi; 3 dpi	RNA-Seq	834, 12 dpi 1053, 72 dpi	810, 12 dpi 1872, 12 dpi	[43]
Epinephelus moara	Liver; spleen; head kidney	natural infection	RNA-Seq	77, liver 89, spleen 318 kidney	6, liver 161, spleen 5314, kidney	[44]
Dicentrarchus labrax	Brain; head kidney	24 hpi; 3 dpi	RNA-Seq	N/A	N/A	[45]
Dicentrarchus labrax	Brain; head kidney	24 hpi; 3 dpi	RNA-Seq	196, head kidney 800, brain	44, head kidney 193, brain	[46]
Lates calcarifer	Head kidney	2 dpi; 15 dpi	RNA-Seq	N/A	N/A	[47]
Epinephelus coiodes	Larvae whole	5 dpi	RNA-Seq	17,939	2526	[48]
Dicentrarchus labrax	Head kidney; Brain	1, 3, 5, 7 dpi	OpenArray® chip	N/A	N/A	[6]
Solea senegalensis	Head kidney; eye/Brain	2 dpi; 3 dpi	OpenArray® chip	N/A	N/A	[49]
Sparus aurata	Larvae whole	6 hpi; 12 hpi; 24 hpi; 48 hpi	RNA-Seq	148, 12 dpi	158, 12 dpi	[50]
Lateolabrax japonicus	Lateolabrax japonicus brain cells	12 hpi; 48 hpi	RNA-Seq	35, 12 dpi 52, 48 dpi	54, 12 dpi 50, 48 dpi	[51]