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The absolute value of "Fold-change" is the magnitude of up- or down-regulation for each gene/homolog after WED immunization.
To identify the differentially expressed genes, the transcriptome data of zebrafish liver from two days after WED immunization and mock immunization were analyzed by using the DESeq package in R software [ 32].
The KEGG results revealed that eight genes involved in the MHC-I pathway were up-regulated, and six genes involved in the MHC-II pathway were down-regulated by two days after WED immunization.
Both the RNA-seq results and qPCR data from our study of zebrafish liver during the early stage after WED immunization indicated that activation of the MHC-I processing pathway in teleosts could elicit cellular immune responses for protection.
In general, based on the results from GO analysis (by BiNGO plugin) and KEGG pathway analysis, the up- and down-regulated genes that were highly related to immune response of fish after WED immunization, significantly grouped into acute phase response (APR), complement activation, immune/defense response, and antigen processing and presentation pathway.
In the study described herein, the genes encoding PA28 subunit 1, PA28 subunit 2 and PA28 subunit 3 were all up-regulated in zebrafish liver, which suggested a shift toward MHC class I antigen processing occurred at the early stage after WED immunization.
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