Table 1. Characteristics of all transcripts analyzed in detail in this study.
| Name | Wnt3-MO response (z-score) | Identity/domains | Cnidarian specificity for novel transcripts | Domains | Expression pattern type | DGE class |
| TRANSCRIPTS UNDER-EXPRESSED IN Wnt3-MO | ||||||
| WegO1 | −24.6 | Cnidarian-restricted | Clytia | O | 1 | |
| Znf845 | −21.2 | Zn-finger domain, expressed in Hydra i-cells | DNA binding | IE | 2 | |
| DMRT-E | −19.1 | DM-DNA binding domain. Doublesex and mab-3 related transcription factor | DNA binding | IE | 2 | |
| HlhIE1 | −18.7 | HLH domain | DNA binding | IE | 1 | |
| Mos3 | −18.2 | Mos kinase | IE | 2 | ||
| Bra2 | −18 | Brachyury 2 ; T-box transcription factor | DNA binding | O | 1 | |
| Sulf | −17.5 | Extracellular Sulfatase related to Sulf1/Sulf2 (modulates ligand signalling) | Signal peptide | IE | 1 | |
| FoxA | −16.2 | FoxA; Forkhead-domain transcription factor | DNA binding | IE | 2 | |
| FoxC | −15.5 | FoxC; Forkhead-domain transcription factor | DNA binding | IE | 2 | |
| ZnfO | −14.8 | Zn-finger domain | DNA binding | O | 2 | |
| Sox15 | −14.5 | Sox domain (Jager et al 2010) | DNA binding | IE | 2 | |
| WntX1A | −13.8 | Wnt ligand, (Momose et al 2008) | Signal peptide | O | 1 | |
| Akr | −13.6 | Small protein with 2 Ankyrin repeats. | O (+ endo) | 1 | ||
| WegIE1 | −13.3 | Cnidarian-restricted , SAM domain | Hydrozoan | IE | 2 | |
| HlhIE2 | −12.9 | HLH domain | DNA binding | IE | 2 | |
| Aat | −12.4 | Amino acid transporter | Trans-membrane | O (+ endo) | 1 | |
| WegIE2 | −12 | Cnidarian-restricted, secreted protein | Clytia | Signal peptide | IE | 2 |
| WegO2 | −11.8 | Cnidarian-restricted | Clytia | O | 1 | |
| Myb | −11.4 | Myb-type HTH DNA-binding domain | DNA binding | O | 1 | |
| Erg | −11.2 | Ets DNA-binding domain, SAM/pointed domain | DNA binding | IE | 2 | |
| Bra | −10.6 | Brachyury 1; T-box transcription factor (Momose & Houliston, 2007) | DNA binding | O | 1 | |
| FoxQ2c | −8.4 | Forkhead-domain transcription factor | DNA binding | IE | 2 | |
| NotumO | −8.4 | Notum ; extracellular Wnt signalling regulator | Signal peptide | O | 1 | |
| WegO3 | −5 | related to human CXorf65 (uncharacterized) | O (+ endo) | 1 | ||
| Gsc | −4.6 | Goosecoid, homeodomain protein | DNA binding | O | 1 | |
| TRANSCRIPTS OVEREXPRESSED IN Wnt3-MO EMBRYOS | ||||||
| Botch1 | 18.1 | ChaC domain - related to Botch (Notch antagonist) | D | 4 | ||
| bZip | 12 | bZip TF, related to CCAAT/enhancer-binding proteins | DNA binding | D/A | 4 | |
| FoxQ2a | 11 | Forkhead-domain transcription factor (Chevalier et al 2006) | DNA binding | A | 3 | |
| Dkk | 10.2 | Dickkopf family (secreted Wnt antagonist) | Signal peptide | A# | 3 | |
| ZnfA | 10 | Zn-finger domain (SP1 family) | DNA binding | A | 3 | |
| NotumA | 9.3 | Notum ; extracellular Wnt signalling regulator | Signal peptide | A | 4 | |
| Botch2 | 8.8 | ChaC domain - related to Botch (Notch antagonist) | D/A | 4 | ||
| WegD1 | 8.2 | Cnidarian-Restricted - Pleckstrin Homology domain | Hydrozoan | D | 4 | |
| WegAI | 8.3 | DUF3504 domain | Cnidarian | A | 3 | |
| Asp | 7.9 | Asparaginase, 5 Ankyrin repeats | D | 4 | ||
| WegD2 | 7.8 | Cnidarian-restricted | Clytia | D | 4 | |
| Dan1 | 7.3 | Dan/Cerberus family of secreted Wnt/BMP inhibitors | Signal peptide | A | 3 | |
| ZpdA | 7.3 | Cell Surface Glycoprotein - zona pellucida domain superfamily | Trans-membrane | D/A | 4 | |
| Amt | 6.9 | Ammonium transporter | Trans-membrane | D | 4 | |
| HD02 | 7 | Antp family homeodomain protein (Chiori et al., 2009) | DNA binding | D | 4 | |
| WegA2 | 6.9 | Cnidarian-restricted , SAM domain | Clytia | A | 3 | |
| Notch | 6.7 | Notch | Trans-membrane | D/A | 3 | |
| UCP | 6.8 | Mitochondrial Uncoupling Protein | D | 4 | ||
| Tbx | 6.5 | T-box transcription factor | DNA binding | A | 3 | |
| sFRP-A | 6.2 | Secreted Fz (sFRP)- lectin domain | Signal peptide | A | 3 | |
| Fz3 | 5.4 | Fz family receptor (Momose & Houliston, 2007) | Signal peptide | A | 3 | |
Details of transcripts for which in situ hybridization analyses were performed previously or in this study, with corresponding expression pattern type (see Figure 4) and DGE class as defined according to z-scores in Wnt3-MO and Fz1-MO transcriptomes compared to non-injected embryos (see Figure 7). Transcripts selected from outside the “top 20” under and over-expressed list are in italics. See text for details. O = Oral; A = Aboral; IE = Ingressing/Endodermal; D = Delayed. endo = endoderm in 48hpf planula. # = no expression detectable in Early Gastrula.