Table 2.
Selected cDNAs1 from all 3 forward (enriched for genes up-regulated by heat-shock) SSH libraries representing stress response related genes
| BLASTx identification4 of selected contigs | |||||||
|---|---|---|---|---|---|---|---|
| Contig ID (Accession Number) | Tissue (Library) | QPCR | # ESTs | Gene Name [Species of best BLASTx Hit] | %ID (aa length of align.) | E-value | Gene Ontology or function of putative orthologue7 |
| 16.C1 (ES784003) | Muscle (gmnlmfta) | Fig.5D2 | 13 | Enolase 3 (beta muscle) [Danio rerio] | 91% (159/174) | 2e-81 | Glycolysis (BP), Cytoplasm (CC) |
| 76.C1 (ES784315) | Muscle (gmnlmfta) | Fig.5C2 | 8 | Translationally-controlled tumor protein5 [Cyprinus carpio] | 68% (116/170) | 9e-62 | Calcium binding and apoptosis regulation [58] |
| 45.C1 (ES783752) | Muscle (gmnlmfta) | Fig.4E2 | 7 | Heat Shock Protein 47 [Onchorhynchus mykiss] | 75% (132/174) | 2e-76 | Serine-type endopeptidase inhibitor activity (MF) |
| 31.C1 (ES783410) | Muscle (gmnlmfta) | Fig.5B2 | 7 | Chaperonin containing TCP1, subunit 5 (epsilon) (synonym: CCT 5) [Danio rerio] | 93% (149/159) | 2e-98 | Protein folding (BP)* |
| 27.C1 (ES783916) | Muscle (gmnlmfta) | Not sig.3 | 5 | Phosphofructokinase, muscle a [Danio rerio] | 88% (173/195) | 4e-98 | Glycolysis (BP)* |
| 79.C1 (ES781823) | Liver (gmnllfta) | Not done | 5 | Cyclophilin A6 [Argopecten irradians] | 80% (132/164) | 2e-75 | Protein folding (BP)* |
| 37.C1 (ES780395) | H. Kidney (gmnlkfta) | Not Done | 5 | Taldo1 protein5,6 (synonym: transaldolase) [Danio rerio] | 82% (120/145) | 6e-63 | Pentose-phosphate shunt (BP)* |
| 65.C1 (EY973473) | H. Kidney (gmnlkfta) | Fig.4A2 | 4 | Heat shock protein 90 alpha [Paralichthys olivaceus] | 93% (93/99) | 5e-47 | Protein folding (BP)*, Response to stress (BP)* |
| 62.C1 (ES781078) | Liver (gmnllfta) | Not done | 4 | Glutathione S-transferase pi5 [Carassius auratus] | 69% (46/66) | 9e-14 | Metabolic process (BP)* |
| 24.C1 (ES781741) | Liver (gmnllfta) | Not done | 4 | T-complex protein 1 subunit beta6 [Salmo salar] | 88% (174/196) | 2e-77 | Protein folding (BP)* |
| 41.C1 (EY973602) | H. Kidney (gmnlkfta) | Not done | 3 | Copper/zinc superoxide dismutase [Epinephelus coioides] | 82% (125/152) | 2e-71 | Superoxide metabolic process (BP), Superoxide dismutase activity (MF)8 |
| 113.C1 (ES781350) | Liver (gmnllfta) | Fig.4B2 | 3 | Heat shock protein 90 kDa beta, member 15,6 (synonym: GRP94) [Danio rerio] | 91% (122/134) | 4e-54 | Protein folding (BP), Response to stress (BP)* |
| 146.C1 (ES781990) | Liver (gmnllfta) | Fig.5A2 | 2 | T-complex 16 (synonym: CCT 1) [Pan troglodytes] | 98% (59/60) | 3e-28 | Assists folding of tubulin and other cytoskeleton proteins [56] |
| 128.C1 (ES783784) | Muscle (gmnlmfta) | Fig.4C2 | 2 | HSP70-1 protein6 (synonym: HSPA1A) [Oryzias latipes] | 92% (170/183) | 7e-76 | Response to stress (BP)*, ATP binding (MF) |
| 5.C1 (EX190083) | H. Kidney (gmnlkfta) | Not done | 2 | TCP1-theta6 [Notothenia coriiceps] | 90% (56/62) | 2e-25 | Protein folding (BP), Protein binding (MF)9 |
| 10.C1 (ES781650) | Liver (gmnllfta) | Fig.4D2 | 2 | 78 kDa glucose-regulated protein6 (synonym: GRP78) [Salmo salar] | 98% (60/61) | 1e-28 | ATP binding (MF), Ig chain folding [39]10 |
| 27.C1 (ES780987) | Liver (gmnllfta) | Not sig.3 | 2 | Aldolase B5 [Poecilia reticulata] | 91% (45/49) | 8e-20 | Glycolysis (BP)11 |
| 84.C1 (ES781112) | Liver (gmnllfta) | Not done | 2 | Pdia4 protein6 [Danio rerio] | 77% (71/92) | 5e-36 | Cell redox homeostasis (BP)* |
| 172.C1 (ES781772) | Liver (gmnllfta) | Not done | 2 | Phosphoglucomutase 1 [Danio rerio] | 96% (38/41) | 1e-14 | Carbohydrate metabolic process (BP)* |
| 174.C1 (EX190172) | H. Kidney (gmnlkfta) | Not done | 2 | Glycogen phosphorylase [Oreochromis mossambicus] | 84% (69/82) | 4e-34 | Carbohydrate metabolic process (BP)* |
1ESTs from each individual forward library (e.g. liver) were assembled separately. Contigs identified in the forward library that were also found in the liver reverse library were included in this table if present as one contig of 2 or more ESTs in at least 2 forward libraries or if validated by QPCR. For genes represented by multiple contigs in a given library or across tissues (i.e. in different forward libraries), the contig with the highest number of contributing sequences is shown. Possible reasons for the presence of multiple contigs with the same gene name within a given library are provided in the discussion. All SSH contigs and singletons for the 3 libraries with all BLASTx statistics and GenBank accession numbers are presented in Additional file 1, Table S1. The GenBank accession number of one representative EST from each contig is given in this table. The names of these SSH libraries in the CGP EST database are gmnllfta (liver), gmnlkfta (head kidney), gmnlmfta (muscle).
2These genes showed at least one statistically significant difference between 2 groups and/or time points (e.g. CT at BHS versus CT at CS, or CT at CS versus HS at CS) in at least 1 tissue.
3These 2 genes were analyzed with QPCR at the individual level, but the data is not presented because there were no statistically significant differences between groups and/or time points.
4The BLASTx hit with the lowest E-value and a gene name (e.g. not predicted or hypothetical) is shown. BLAST statistics were collected on the 4th of December, 2008 and reflect the entries in the nr protein database up to that date. aa = amino acids.
5These cDNAs were represented by a contig or a singleton in the liver reverse library.
6Synonyms for protein names were retrieved from the Swiss-Prot Protein Knowledgebase Database http://ca.expasy.org/sprot/: Cyclophilin A: Peptidyl-prolyl-isomerase A, PPIase.
Taldo1 protein: Transaldolase 1.
T-complex protein 1 subunit beta: CCT2.
Heat shock protein 90 kDa beta, member 1: HSPB1, Chaperone protein GP96, Tumor rejection antigen (gp96) 1.
T-complex 1: Chaperonin-containing T-complex polypeptide alpha subunit.
HSP70-1: HSP70, Heat Shock Protein 70 kDa 1, HSP72.
TCP1-theta: T-complex protein 1 subunit theta, CCT8.
Glucose-regulated protein 78 kDa: Heat Shock Protein 70 kDa protein 5.
Pdia4 protein: Protein disulfide isomerase-associated 4.
7Functional annotation associated with the cod cDNA's best BLAST hit or an annotated putative orthologue from Homo sapiens or Mus musculus (* or reference in []). Gene ontology (GO) categories: Biological Process (BP), Molecular Function (MF) and Cellular Component (CC).
8Other functional annotations associated with this cod EST are: Endoplasmic reticulum (CC) and Nucleotide binding (MF).
9Other functional annotations associated with this cod EST are: Oxireductase activity (MF), Zinc ion binding (MF) and Copper ion binding (MF).
10Other functional annotations associated with this cod EST are: Cellular protein (CC), Cytoplasm (CC), Metabolism (BP), ATP binding (MF), Nucleotide binding (MF).
11Other functional annotations associated with this cod EST are: Catalytic activity (MF), Fructose biphosphate aldolase activity (MF) and Metabolic process (BP).