Impact of selenium supplementation on fish antiviral responses: a whole transcriptomic analysis in rainbow trout (Oncorhynchus mykiss) fed supranutritional levels of Sel-Plex®

Pacitti, D.; Lawan, M. M.; Feldmann, J.; Sweetman, J.; Wang, T.; Martin, S. A. M.; Secombes, C. J.

doi:10.1186/s12864-016-2418-7

Table 4 List of selected transcripts that were significantly modulated in the HK of fish fed the Sel-Plex enriched diet²

From: Impact of selenium supplementation on fish antiviral responses: a whole transcriptomic analysis in rainbow trout (Oncorhynchus mykiss) fed supranutritional levels of Sel-Plex®

Trait	SeC	SeP	CP	SeP⁵	Acc. Number⁶	Identity⁷	HGNC	Gene Function⁹
Identifier¹	HK²	HK³	HK⁴	CP	Acc. Number⁶	Identity⁷	Symbol⁸	Gene Function⁹
TC171135	4.2	−1.6	−1.1	3.0	XM_001922673	Ring finger protein 111	RNF111	Enzyme linked receptor protein signaling pathway
TC171135	4.2	−1.6	−1.1	3.0	XM_001922673	Ring finger protein 111	RNF111	macromolecule catabolic process
CUST_216_	3.7	−1.1	2.8	1.2	NM_1195534.1	MHC class II beta chain	HLA-DPB1	Cellular response to organic substance
PI429021944	3.7	−1.1	2.8	1.2	NM_1195534.1	MHC class II beta chain	HLA-DPB1	Cellular response to chemical stimulus
TC155958	2.5	−2.4	−1.1	1.2	DQ683253	Protein tyrosine phosphatase alpha	PTPRA	Cellular response to organic substance
TC155958	2.5	−2.4	−1.1	1.2	DQ683253	Protein tyrosine phosphatase alpha	PTPRA	Enzyme linked receptor protein signaling pathway
TC132551	2.2	−1.8	1.2	1.0	NM_001124648	Insulin-like growth factor binding protein 1	IGFBP7	Cellular response to organic substance
TC132551	2.2	−1.8	1.2	1.0	NM_001124648	Insulin-like growth factor binding protein 1	IGFBP7	Cellular response to chemical stimulus
TC150601	2.2				AF062496	Insulin receptor a	INSR	Glucose metabolic process
TC150601	2.2				AF062496	Insulin receptor a	INSR	Hexose metabolic process
TC153429	−2.3	6.5	1.9		NM_001141739	Aspartate aminotransferase cytoplasmic	GOT1	Monosaccharide biosynthetic process
TC153429	−2.3	6.5	1.9		NM_001141739	Aspartate aminotransferase cytoplasmic	GOT1	Gluconeogenesis
TC155657	6.2	−1.2	1.3	4.1	BT072052	Thioredoxin domain-containing protein 5	TXNDC5	Intracellular transport
TC134082	5.0				NM_200685	Nucleoporin 98	NUP98	Nuclear transport
TC134082	5.0				NM_200685	Nucleoporin 98	NUP98	cellular protein complex assembly
TC167412	3.6	−1.1	1.3	2.5	NM_001177932	SEC24 family member D	SEC24D	Cytoplasmic transport
TC167412	3.6	−1.1	1.3	2.5	NM_001177932	SEC24 family member D	SEC24D	Macromolecular complex assembly
TC141904	2.8	2.3	5.2	1.2	NM_001124423	C-x-c chemokine receptor type 3B variant 1	CXCR3	Maintenance of location
TC147797	2.1	1.4	2.0	1.5	NM_201305	Karyopherin alpha 4	KPNA4	Cytoplasmic transport
TC147797	2.1	1.4	2.0	1.5	NM_201305	Karyopherin alpha 4	KPNA4	Nuclear transport
TC164726	2.0				NM_001025530	SEC62 homolog	SEC62	Intracellular transport
TC146558	3.8	−1.4	1.6	1.7	NM_001141745	Splicing factor 3a subunit 1	SF3A1	mRNA splice site selection
TC146558	3.8	−1.4	1.6	1.7	NM_001141745	Splicing factor 3a subunit 1	SF3A1	Spliceosomal complex assembly
TC171125	2.3	1.0	2.5	−1.1	NM_001173829	Tuftelin-interacting protein 11	TFIP11	Spliceosomal complex
TC171125	2.3	1.0	2.5	−1.1	NM_001173829	Tuftelin-interacting protein 11	TFIP11	Ribonucleoprotein complex organization
TC147076	2.3	1.2	2.7	−1.0	NM_001139882	Cleavage and polyadenylation specific factor 3	CPSF3	mRNA splicing, via spliceosome
TC147076	2.3	1.2	2.7	−1.0	NM_001139882	Cleavage and polyadenylation specific factor 3	CPSF3	RNA splicing, via transesterification reactions
TC143716	2.1				BT072055	RNA-binding protein 5	RBM5	Spliceosomal complex assembly
TC143716	2.1				BT072055	RNA-binding protein 5	RBM5	ribonucleoprotein complex organization
TC142487	2.0	1.3	3.0	−1.1	NM_001173772	Polyadenylate-binding protein 2	PABPN1	mRNA splicing, via spliceosome
TC142487	2.0	1.3	3.0	−1.1	NM_001173772	Polyadenylate-binding protein 2	PABPN1	RNA splicing, via transesterification reactions
TC171058	−4.1	−1.0	−3.2	−1.3	NM_001165069	U1 small nuclear ribonucleoprotein C	SNRPC	mRNA splice site selection
TC161955	5.0	−1.9	1.4	1.9	BT059981	Hemoglobin subunit alpha-4	HBA1	Protein complex assembly
TC161955	5.0	−1.9	1.4	1.9	BT059981	Hemoglobin subunit alpha-4	HBA1	Protein maturation
TC156216	4.9	−1.4	3.5	1.0	NM_214766	Mediator of RNA polymerase II	MED25	Protein/macromolecular complex assembly
TC161655	3.7	−1.5	2.1	1.2	NM_001137665	NCK-associated protein 1	NCKAP1	Protein/macromolecular complex assembly
TC136900	3.6	−1.7	2.2	−1.0	NM_213485	Cullin-associated and neddylation-dissociated 1	CAND1	Protein/macromolecular complex assembly
IMM 315	3.3	−1.8	2.3	−1.3	BT072012	Myeloperoxidase	MPO	Cellular protein complex assembly
IMM 315	3.3	−1.8	2.3	−1.3	BT072012	Myeloperoxidase	MPO	Myofibril
TC135948	3.2	−1.2	−1.1	2.9	NM_001140517	Proteinase-activated receptor 2	F2RL1	Cellular protein complex assembly
TC135948	3.2	−1.2	−1.1	2.9	NM_001140517	Proteinase-activated receptor 2	F2RL1	Mitotic cell cycle phase transition
TC138630	10.3	−1.1	1.8	5.2	BT049107	Protease regulatory subunit 4	PSMC1	ATPase activity
TC138630	10.3	−1.1	1.8	5.2	BT049107	Protease regulatory subunit 4	PSMC1	Mitotic cell cycle phase transition
TC159410	9.3	1.2	8.9	1.2	not-annotated	not-annotated	SMARCAD1	Nucleoside-triphosphatase activity
TC159410	9.3	1.2	8.9	1.2	not-annotated	not-annotated	SMARCAD1	Pyrophosphatase activity
TC157271	5.2	−2.5	1.5	1.4	XM_001920063	Myosin heavy polypeptide 9b non-muscle	MYH9	ATPase activity
TC157271	5.2	−2.5	1.5	1.4	XM_001920063	Myosin heavy polypeptide 9b non-muscle	MYH9	Hemopoiesis
TC171400	3.5	−1.1	1.3	2.3	NM_001140090	PDZ domain-containing protein 1	KIF1B	ATPase activity
TC171400	3.5	−1.1	1.3	2.3	NM_001140090	PDZ domain-containing protein 1	KIF1B	Nucleoside-triphosphatase activity
TC155666	3.4	−1.3	1.8	1.5	BT050023	Protease regulatory subunit 8	PSMC5	ATPase activity
TC155666	3.4	−1.3	1.8	1.5	BT050023	Protease regulatory subunit 8	PSMC5	Mitotic cell cycle phase transition
TC158128	−4.1				BT060239	Rho-related GTP-binding protein	RHOQ	Nucleoside-triphosphatase activity
TC158128	−4.1				BT060239	Rho-related GTP-binding protein	RHOQ	Pyrophosphatase activity
TC169119	3.0				BT045702	Tubulin alpha chain	TUBA1A	Cellular protein complex assembly
TC169119	3.0				BT045702	Tubulin alpha chain	TUBA1A	Mitotic cell cycle phase transition
TC163518	2.8	1.0	4.3	−1.5	NM_001140179	Targeting protein for Xklp2	TPX2	Mitotic cell cycle process
TC154893	2.7				CU861476	Adenomatous polyposis coli	APC	Cellular protein complex assembly
TC154893	2.7				CU861476	Adenomatous polyposis coli	APC	Maintenance of location
TC166756	2.2	−1.2	1.4	1.3	NM_001140263	Lissencephaly-1 homolog B	PAFAH1B1	Cellular component disassembly
TC166756	2.2	−1.2	1.4	1.3	NM_001140263	Lissencephaly-1 homolog B	PAFAH1B1	Mitotic cell cycle phase transition
TC163683	2.2	1.5	2.1	1.6	NM_001139958	Cell division cycle 27	CDC27	Mitotic cell cycle phase transition
TC163683	2.2	1.5	2.1	1.6	NM_001139958	Cell division cycle 27	CDC27	Mitotic cell cycle process
TC169614	−2.4	1.7	−2.0	1.4	AB076182	Myosin heavy chain	TUBB	Mitotic cell cycle phase transition
TC169614	−2.4	1.7	−2.0	1.4	AB076182	Myosin heavy chain	TUBB	Cellular protein complex assembly
TC157158	4.2				NM_001140534	Transketolase	TKT	Monosaccharide biosynthetic process
TC157158	4.2				NM_001140534	Transketolase	TKT	Glucose metabolic process
TC137888	3.7	1.3	7.8	−1.6	NM_001173578	SMEK homolog 2 suppressor of mek1	SMEK1	Monosaccharide biosynthetic process
TC137888	3.7	1.3	7.8	−1.6	NM_001173578	SMEK homolog 2 suppressor of mek1	SMEK1	Gluconeogenesis
TC164289	2.4	2.4	6.2	−1.1	AF246148	6-phosphofructo-2-kinase/	PFKFB3	Glucose metabolic process
TC164289	2.4	2.4	6.2	−1.1	AF246148	fructose-2,6-biphosphatase 9	PFKFB3	Hexose metabolic process
TC157094	2.4				BT072470	UDP-N-acetylglucosamine-peptide N-acetylglucosaminyltransferase 110 kDa subunit	OGT	Monosaccharide biosynthetic process
TC157094	2.4				BT072470		OGT	Glucogenesis
TC150298	−3.6				NM_131108	Type I cytokeratin	KRT17	Monosaccharide biosynthetic process
TC150298	−3.6				NM_131108	Type I cytokeratin	KRT17	Gluconeogenesis
TC156671	−3.7	1.6	−2.9	1.2	NM_001128704	Pyruvate dehydrogenase kinase, isozyme 4	PDK2	Monosaccharide biosynthetic process
TC147626	5.5	−1.4	1.6	2.4	CR382377	B-cell CLL/lymphoma 11Ba	BCL11B	Hemopoiesis
TC147626	5.5	−1.4	1.6	2.4	CR382377	B-cell CLL/lymphoma 11Ba	BCL11B	Cell homeostasis
TC169770	2.6	1.2	3.6	−1.2	NM_001141785	Replication protein A 70 kDa DNA-binding subunit	RPA1	Mitotic cell cycle phase transition
TC169770	2.6	1.2	3.6	−1.2	NM_001141785	Replication protein A 70 kDa DNA-binding subunit	RPA1	Cell homeostasis
TC140328	2.2				DQ143177	NOTCH protein-like	NOTCH2	Hemopoiesis
TC140328	2.2				DQ143177	NOTCH protein-like	NOTCH2	Notch signaling pathway
IMM 476	2.0	−1.3	1.1	1.4	NM_001160476	Precursor of second macrophage	CSF1	Hemopoiesis
IMM 476	2.0	−1.3	1.1	1.4	NM_001160476	colony-stimulating factor	CSF1	Cell homeostasis
TC138601	2.0				NM_001140256	TGF-beta receptor type-2	TGFBR2	Hemopoiesis
TC138601	2.0				NM_001140256	TGF-beta receptor type-2	TGFBR2	Hematopoietic/lymphoid organ development
IMM 581	−2.2				NM_001185029	Interleukin 17C1	IL17C	Hemopoiesis
TC167544	6.8	1.9	6.8	1.9	AF542091	Low density lipoprotein receptor	LDLR	Cell homeostasis
TC167544	6.8	1.9	6.8	1.9	AF542091	Low density lipoprotein receptor	LDLR	Viral process
TC133169	5.6	−2.0	1.1	2.5	FM207660	Partial nIL-1 F gene for novel IL-1 cytokine	ACE2	Viral process
TC133169	5.6	−2.0	1.1	2.5	FM207660	family member exon 8	ACE2	Protein maturation
TC136993	4.6	1.3	3.1	1.9	BT048700	Vesicle-associated membrane	VAPB	Viral process
TC136993	4.6	1.3	3.1	1.9	BT048700	protein-associated protein B	VAPB	Symbiosis, through parasitism
TC157378	2.5	−1.5	−1.4	2.4	BT057398	SNARE-associated protein Snapin	SNAPIN	Viral process
TC157378	2.5	−1.5	−1.4	2.4	BT057398	SNARE-associated protein Snapin	SNAPIN	Symbiosis, through parasitism
TC137075	2.3	−1.6	−1.2	1.8	AB208639	AB11 family interacting protein 4 (class II) a	RAB11FIP4	Viral process
TC137075	2.3	−1.6	−1.2	1.8	AB208639	AB11 family interacting protein 4 (class II) a	RAB11FIP4	Symbiosis, through parasitism
TC160444	2.3				HQ206612	Structure specific recognition protein 1	SSRP1	Viral process
TC160444	2.3				HQ206612	Structure specific recognition protein 1	SSRP1	Symbiosis, through parasitism

The selection was based on the results of the GO analysis (Fig. 6). Genes with a corresponding microarray feature code¹ found involved in a biological process significantly altered by the experimental diet in the HK were selected. If the transcripts were significantly modulated also in fish fed the experimental diet enriched with and injected with poly(I:C)³, or in the same tissue of fish fed the control diet and injected with poly(I:C)⁴, these values are given. Also the fold change of the expression of the same targets between these last two groups is reported, as given from Genespring software⁵. All the transcripts shown were significantly modulated at p < 0.05 following the Benjamini–Hochberg correction and had a fold change ≥2. Accession numbers of the cDNA sequences⁶, their identity⁷ and the corresponding human orthologue⁸ determined by BLASTx within the Ensemble database are reported. For each gene the function assigned by ClueGO software is also indicated. SeC represents the groups comparison addressed to analyse the effects of the Sel-Plex enriched diet. CP and SeP instead represent the comparisons addressed to analyse the effect of poly(I:C) stimulation on fish fed either a control diet or the experimental diet respectively

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