Table 1.
Comparison of significant normalized enrichment scores (NESs) of gene sets (GSs) for rag1−/− genotype/spring viremia carp virus (SVCV)-infected phenotypes of adult zebra fish by gene set enrichment analysis (GSEA).
| GS | GSor | A | B | C | 1 | 2 | 3 | 4 |
|---|---|---|---|---|---|---|---|---|
| 5IFN + 4MX | L | 2.31** | −1.53* | 1.63* | X | X | ||
| 7IFN + 5MX5 + 8TLR | L | 2.25** | −1.50* | 1.22 | X | X | ||
| 2348TLR + 12IFN | L | 2.20** | −1.83** | 0.77 | X | |||
| 9CXCS (chemokines) | L | 2.13** | −1.42 | 0.96 | ||||
| MX (myxovirus-induced proteins) | KW | 2.13** | −1.56 | 0.95 | X | X | ||
| IFN (interferon) | KW | 1.93** | −1.25 | 1.50 | X | |||
| 278CASP (caspases) | L | 1.88** | −1.86** | −0.97 | X | |||
| NITR (novel immune-type receptors) | KW | 1.88** | −1.88** | 1.04 | X | |||
| Type II interferon signaling (ifng) | W | 1.84** | −1.43 | −0.76 | X | |||
| MHC (major histocompatibility complex) | KW | 1.83** | −0.88 | −0.99 | ||||
| 7ONCOS (oncogenes) | L | 1.76** | −2.01** | 0.85 | ||||
| 7TLR7CASP (toll-like recpt + caspases) | L | 1.74** | −1.28 | 2.20** | X | |||
| Cytosolic DNA-sensing pathway | K | 1.69** | −1.42 | 0.84 | ||||
| Intestinal immune network IgA | K | 1.62** | −1.40 | 1.34 | ||||
| AMP (antimicrobial peptides) | KW | 1.61** | 1.18 | 1.74** | ||||
| Apoptosis modulation by hsp70 | W | 1.59** | −1.16 | 0.79 | X | |||
| CHK (chemokines) | KW | 1.57** | −0.72 | 1.37 | ||||
| 1CREB (transcription factors) | L | 1.46* | −1.93** | −1.43 | ||||
| Proteasome degradation | W | 1.19 | 1.98** | 1.16 | X | |||
| COM (complement) | KW | 0.82 | 1.37** | 1.23 | X | |||
| Complement and coagulation cascades | K | −1.03 | 1.94** | 1.79** | X | |||
| 1NFKB2NFKBIAB (NF-kB related) | L | −1.60* | −1.06 | −3.07** | ||||
| CRP (c-reactive proteins) | KW | −2.20** | 1.60** | −0.68 | X | |||
| 7MAPKS (MAP kinases) | L | −2.30** | 2.33** | −1.10 | ||||
| 1IG3MAPK (MAP kinases) | L | −2.40** | 2.01** | −2.05** |
The immune-targeted in-house-designed microarray, Agilent’s ID47562 in a 8 × 15 K format deposited in GEO’s GPL17670 was used. Raw and normalized data were deposited in the GEO’s GSE54096. GSor, GS origin. K, GS retrieved from human orthologous KEGG pathways. W, GS retrieved from human orthologous WIKI pathways. KW, GS retrieved from the GenBank data by searching zebra fish (Danio rerio) mRNA with key-words, briefly described within parenthesis. L, novel GS proposed by leading edge gene analysis (LEGA) of the differential transcription profiles from different zebra fish genotypes/phenotypes, including those previously described (26). The numbers before the LEGA gene names indicate the number of those genes in each GS. The significantly modulated GS were ordered by their NES values in (A). **False discovery rate (FDR) q value < 0.05. *FDR q value < 0.25. (A) rag1−/− versus rag1+/+ genotypes. (B) SVCV-infected rag1−/− phenotype versus rag1−/− genotype. (C) SVCV-infected rag1+/+ phenotype versus rag1+/+ genotype. 1, GS of interferon-related TLR + IFN + MX genes. 2, GS related to apoptosis/caspases (gray rows). 3, GS related to complement. 4, GS related to multigene families modulated in VHSV survivors. 5, GS related to multigene families modulated in VHSV survivors.