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Table 1 Identification and transcript expression results for 14 microarray-identified features selected for QPCR studya

From: Transcriptome profiling reveals that feeding wild zooplankton to larval Atlantic cod (Gadus morhua) influences suites of genes involved in oxidation-reduction, mitosis, and selenium homeostasis

Microarray probe IDb Protein name (species affiliation, GenBank accession number, and associated E-value for the best named BLASTx hit)c Functional annotation associated with best named BLASTx hitd Microarray fold change in RA-Zoo versus: QPCR fold change in RA-Zoo versuse:
RA RA-PH RA RA-PH
37395 Glutathione peroxidase 1b (Sparus aurata, AFY97791, 1.81E-101) Response to oxidative stress (BP); oxidation-reduction process (BP); peroxidase activity (MF); glutathione peroxidase activity (MF); oxidoreductase activity (MF). 2.57 2.68 2.66 3.33
42046 Selenoprotein Pa (Oncorhynchus mykiss, CCX35038, 1.97E-54) NA 3.31 3.89 4.10 5.34
42811 Trypsinogen H1_3a1 (Dissostichus mawsoni, AEA08590, 2.07E-120) Proteolysis (BP); catalytic activity (MF); serine-type endopeptidase activity (MF); hydrolase activity (MF). 5.62 3.40 3.28 1.88
42084 Aurora kinase B (Danio rerio, NP_997731, 2.47E-33) ATP binding (MF); histone serine kinase activity (MF); metal ion binding (MF); cellular response to UV (BP); chromosome segregation (BP); mitotic cytokinesis (BP); spindle midzone assembly involved in mitosis (BP); multicellular organismal development (BP); negative regulation of B cell apoptotic process (BP); histone H3-S28 phosphorylation (BP); transferase activity (MF)f. 1.79 1.59 1.51 1.54
46230 Nattectin precursor (Anoplopoma fimbria, ACQ58341, 7.10E-31) Carbohydrate binding (MF). 2.04 2.13 2.45 2.58
36829 Dehydrogenase/reductase SDR family member 1 (Salmo salar, NP_001134326; 1.87E-59) Metabolic process (BP); oxidation-reduction process (BP); oxidoreductase activity (MF). −1.60 −2.29 −2.58 −1.96
37900 Cytochrome P450 CYP2Y3 (Danio rerio, AAX37329, 6.47E-90)g Oxidation-reduction process (BP); monooxygenase activity (MF); iron ion binding (MF); oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen (MF); heme binding (MF). −3.14 −2.61 −6.94 −4.99
38166 Microsomal glutathione S-transferase 3 (Oncorhynchus mykiss, ACO07847, 1.25E-73) Metabolic process (BP); transferase activity (MF). −1.88 −1.99 −2.45 −1.79
39283 Peroxiredoxin-1 (alias Natural killer enhancing factor) (Anoplopoma fimbria, ACQ58049, 3.73E-125) Oxidation-reduction process (BP); antioxidant activity (MF); oxidoreductase activity (MF); peroxiredoxin activity (MF). −2.05 −2.51 −2.99 −2.89
41986 DNA-damage-inducible transcript 4 protein (alias REDD1; RTP801) (Dicentrarchus labrax, CBN81525, 9.89E-88) Negative regulation of signal transduction (BP). −3.06 −1.89 −3.88 −2.26
42481 Solute carrier family 6, member 6 (alias Sodium- and chloride-dependent taurine transporter) (Salmo salar, NP_001117102, 1.53E-104) Transport (BP); neurotransmitter transport (BP); organic acid transport (BP); transmembrane transport (BP); neurotransmitter:sodium symporter activity (MF); taurine:sodium symporter activity (MF). −1.84 −1.77 −2.37 −2.33
42540 Thioredoxin-interacting protein (Salmo salar, ACN10667, 1.80E-92) NA −2.02 −2.10 −2.29 −2.38
37201 Ferritin, middle subunit (Salmo salar, ACI66864, 2.69E-12) Iron ion transport (BP); cellular iron ion homeostasis (BP); ferric iron binding (MF). −2.25 −1.86 −2.61 −2.95
36536 Coagulation factor V (Danio rerio, AAN71005, 9.03E-15) Cell adhesion (BP); copper ion binding (MF). −1.98 −2.04 −2.15 −2.30
  1. NA not applicable (i.e. no functional annotation found for best named BLASTx hit)
  2. aThese 14 genes were selected from the list of 303 microarray features that were RA-Zoo responsive compared with both RA and RA-PH in 9 mm stage samples. The complete list of 303 microarray features is available in Additional file 1: Table S1 (147 genes significantly up-regulated in RA-Zoo compared with both RA and RA-PH) and Additional file 2: Table S2 (156 genes significantly down-regulated in RA-Zoo compared with both RA and RA-PH)
  3. bProbe identifier (ID) numbers are 5-digit unique identifiers for the 50mer probes on the Atlantic cod 20K microarray [19]
  4. cThe BLASTx hits with the lowest E-values and protein names (e.g. not “unnamed protein product” or “predicted”) are shown for the Atlantic cod expressed sequence tag (EST) contiguous sequences (contigs) or singletons used for probe design [19]
  5. dFunctional annotation associated with the best named BLASTx hit of the Atlantic cod cDNA sequence represented by the informative microarray probe. Biological Process (BP) and Molecular Function (MF) Gene Ontology (GO) terms are listed in this table. If multiple, similar terms were available, a representative term was selected for inclusion in this table
  6. eQPCR mean fold-change was calculated as mean RA-Zoo relative quantity (RQ) divided by mean RA or RA-PH RQ for genes up-regulated in RA-Zoo, and as mean RA or RA-PH RQ divided by mean RA-Zoo RQ for genes down-regulated in RA-Zoo (indicated by a negative sign). All genes in this table except Nattectin were QPCR validated as significantly (p < 0.05) differentially expressed between RA-Zoo and both RA and RA-PH larvae at the 9 mm stage
  7. fSince there are over 20 GO terms associated with this sequence, a selection of GO terms are included in this table
  8. gThe best named hit was Cytochrome P450 precursor (Danio rerio, NP_001018658). The second-best hit is listed as it has a more descriptive name and a similar E-value