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Table 1 Summary of candidate genes identified from microarray analyses analyzed with in situ hybridization.

From: Spatio-temporal regulation of Wnt and retinoic acid signaling by tbx16/spadetail during zebrafish mesoderm differentiation

Affy Probe ID Gene Namea Gene Symbol Corroborate Microarrayb Expression Domainc Expression in spt Embryosd Expression Studies Previously Reported Identified by Array Fold-Change in Array
Dr.16366.1.S1_at BI430182 e BI430182 f Yes IM downregulated No 4/5s -5.54
Dr.14123.1.A1_at zgc:171560 zgc:171560 f Yes ubiquitous downregulated No 4/5s -4.51
Dr.16573.3.S1_x_at zgc:112524 zgc:112524 f Yes ubiquitous downregulated No 4/5s -3.49
Dr.12443.1.A1_at zgc:92345 zgc:92345 f Yes ubiquitous downregulated No 4/5s -2.73
Dr.1085.2.A1_at zgc:110288 zgc:110288 f Yes ubiquitous downregulated No 4/5s -2.45
Dr.12055.1.S1_at CCAAT/enhancer binding protein (C/EBP), alpha cebpa f Yes IM, ALPM downregulated Yes 4/5s -16.67
Dr.8064.1.S1_at draculin drl Yes IM downregulated Yes 4/5 s and 21s -15.64 and -3.65
Dr.3338.1.S1_at hydroxymethylb ilane synthase a hmbsa f Yes IM, midline structures downregulated Yes 4/5s -4.56
Dr.515.1.A1_at GTP binding protein 1 gtpbp1 f Yes IM, midline structures downregulated Yes 4/5s -2.68
Dr.7908.1.S2_at calmodulin 1a calm1a f, g Yes IM, neuroectoderm downregulated Yes 4/5s -2.11
Dr.4151.1.S1_at Janus kinase 2a jak2a Yes ubiquitous downregulated Yes 4/5s -4.64
Dr.21814.1.S1_at zgc:136864 zgc:136864 No - Category A ubiquitous same No 4/5s -5.73
Dr.1118.1.A1_at zgc:153587 zgc:153587 No - Category A ubiquitous same No 4/5s -4.44
Dr.883.1.A1_at DnaJ (Hsp40) homolog, subfamily C, member 21 dnajc21 No - Category A ubiquitous same No 4/5s -2.52
Dr.14906.1.A1_at zgc:153390 zgc:153390 No - Category A ubiquitous same No 4/5s -2.21
Dr.16120.1.S1_at prostaglandin E synthase 2-like ptgesl No - Category A ubiquitous same Yes 4/5s -4.98
Dr.3023.1.S1_at zinc finger, FYVE domain containing 21 zfyve21 No - Category A ubiquitous same Yes 4/5s -4.47
Dr.8412.1.A1_at DEAD (Asp-Glu-Ala-Asp) box polypeptide 3 ddx3 No - Category A ubiquitous same Yes 4/5s -3.7
Dr.4269.1.A1_at zgc:64161 zgc:64161 No - Category A ubiquitous same Yes 4/5s -3.56
Dr.4468.1.S1_at ribonuclease H2, subunit B rnaseh2b No - Category A ubiquitous same Yes 4/5s -2.97
Dr.7212.1.S1_at nedd8 activating enzyme E1 subunit 1 nae1 No - Category A ubiquitous same Yes 4/5s -2.84
Dr.12643.1.A1_at zgc:77744 zgc:77744 No - Category A ubiquitous same Yes 4/5s -2.71
Dr.15269.1.S1_at zgc:56033 zgc:56033 No - Category A ubiquitous same Yes 4/5s -2.68
Dr.14026.1.A1_at zgc:66110 zgc:66110 No - Category A ubiquitous same Yes 4/5s -2.68
Dr.7237.1.S1_at zgc:63962 zgc:63962 No - Category A ubiquitous same Yes 4/5s -2.51
Dr.7966.1.S1_at ATPase, H+ transporting, lysosomal, V1 subunit E isoform 1 atp6v1e1 f No - Category B polster, neuroectoderm downregulated No 4/5s -2.54
Dr.1791.1.S1_at pdgfa associated protein 1 pdap1 f No - Category B polster downregulated Yes 4/5s -4.25
Dr.14426.1.S1_at pin2/trf1-interacting protein 1 pinx1 f No - Category B polster, neuroectoderm, PM downregulated Yes 4/5s -3.04
Dr.9715.3.S1_a_at exosome component 4 exosc4 f No - Category B PM downregulated Yes 4/5s -3
Dr.7799.1.A1_at zgc:56136 zgc:56136 f No - Category B neuroectoderm downregulated Yes 4/5s -2.73
Dr.18052.1.S1_at zinc finger protein 593 znf593 f No - Category B neuroectoderm, PM downregulated Yes 4/5s -2.46
Dr.893.2.S1_at LOC798291 LOC798291 No - Category C PM same No 4/5s -2.32
Dr.9423.1.S1_at zgc:73329 zgc:73329 No - Category C PM same Yes 4/5s -3.25
Dr.1663.1.A1_at transcription factor 25 (basic helix-loop-helix) tcf25 No - Category C polster same Yes 4/5s -2.76
Dr.8822.1.A1_at zinc finger E-box binding homeobox 2a zeb2a No - Category C neuroectoderm same Yes 4/5s -3.6
Dr.25212.1.A1_at calsyntenin 1 clstn1 No - Category C Kupffer's vesicle, tail bud same Yes 4/5s -3.28
Dr.12545.1.S1_at si:dkey-177p2.6 si:dkey-177p2.6 No - Category C neuroectoderm, PM same Yes 4/5s -2.87
Dr.19223.1.S2_at aldolase c, fructose-bisphosphate aldoc No - Category C neuroectoderm same Yes 4/5s -5.23
Dr.25679.1.S1_at solute carrier family 1 (glial high affinity glutamate transporter), member 3a slc1a3a No - Category C neuroectoderm same Yes 4/5s -3.05
Dr.1002.1.S1_at LOC568423 LOC568423 f No - Category D ubiquitous upregulated No 4/5s -2.34
Dr.25683.5.A1_at sphingosine-1-phosphate receptor 1 s1pr1 f No - Category D neuroectoderm, tailbud upregulated Yes 4/5s -2.76
Dr.8183.1.S1_at homeo box A11a hoxa11a f No - Category D tailbud upregulated Yes 4/5s -2.35
Dr.5206.1.S1_at aldehyde dehydrogenase 1 family, member A2 aldh1a2 Yes PM, eyes downregulated Yes 21s -6.16
Dr.1817.1.A1_at regulator of calcineurin family member 3 rcan3 f Yes PM downregulated Yes 21s -2.72
Dr.23348.1.A1_at bone morphogenetic protein 3 bmp3 f, g Yes PM, neuroectoderm downregulated Yes 21s -1.68
Dr.610.1.S1_at heat shock protein 90-alpha 1 hsp90a.1 f, g Yes PM downregulated Yes 21s -2.26
Dr.345.1.S1_at unc-45 homolog B (C. elegans) unc45b f, g Yes PM downregulated Yes 21s -2.39
Dr.26455.1.S1_at fibroblast growth factor receptor-like 1a fgfrl1a f, g Yes PM, eyes downregulated Yes 21s -1.73
  1. a Gene names are consistent with those in ZFIN (The Zebrafish Model Organism Database, http://zfin.org/) whenever possible.
  2. b "Yes" is defined as intermediate mesoderm expression (for genes from the 4/5s microarray) or paraxial mesoderm expression (for genes from the 21s microarray) that is downregulated in spt. Category A is defined as ubiquitous expression that is not changed in spt. Category B is defined as expression that is downregulated in spt but that is absent from the intermediate mesoderm. Category C is defined as expression that is unchanged in spt and absent from the intermediate mesoderm. Category D is defined as expression upregulated in spt.
  3. c Abbreviations are ALPM (anterior lateral plate mesoderm), IM (intermediate mesoderm) and PM (paraxial mesoderm).
  4. d Downregulated is defined as at least part of the expression domain being reduced compared to the wild type based on visual detection. Upregulated is defined as at least part of the expression domain being enhanced, and no part of the expression domain being reduced, compared to the wild type, based on visual detection.
  5. e EST ID is used here because this Affy probe is annotated by EST only and has not been assigned to an annotated gene. All of the other candidates explored by in situ hybridization have been linked to annotated genes.
  6. f These genes, to our knowledge, have not previously been revealed to act downstream of tbx16.
  7. g These genes were identified as differentially expressed by the unfiltered analyses only; all other candidates explored by in situ hybridization were identified by the filtered analyses.