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Table 2.

Set 1 genes regulated by Smad7 in isolated ectoderm

CloneIdentityIncrease in arrayRT-PCR analysis*Whole-mount in situ hybridization
28-A12 Cytokeratin- type II Four- to fivefold Downregulated Epidermis 
45-A6 Hypothetical protein. DKFZp586 G1123 Sixfold Upregulated Dorsal-neural 
45-G5 Steroidogenic acute regulatory protein-related (STAR) protein Fourfold N/D N/D 
45-G6 Xenopus cold-inducible RNA-binding protein 2 (CIRP-2) Three- to sevenfold Unchanged Neural 
45-H5 Pro-/Para-thymosin alpha homolog Eightfold Upregulated Neural 
46-E2 FUSE/KH-binding protein Fourfold Upregulated Dorsal-neural 
46-G6 No matches Threefold N/D N/D 
47-A4 CTP synthase II Fourfold Upregulated N/D 
47-B11 Plexin/Semaphorin receptor Fourfold Upregulated Dorsal-neural 
47-F3 No matches Fivefold Unchanged Neural 
47-F5 High-mobility-group (HMG)-like protein Four- to fivefold Upregulated N/D 
47-G3 Human hypothetical protein. Threefold Upregulated Dorsal/anterior neural 
47-G6 DG-42 4.5-fold Downregulated Ventral/epidermal 
47-G10 N-acetyl glucosamine transporter Fourfold N/D N/D 
48-A2 Xenopus tight junction TM-protein; Claudin 3 Fourfold Upregulated Published neural 
48-F11 Hypothetical protein. Fourfold Downregulated Dorsal-neural 
49-B2 Xenopus cold-inducible RNA-binding protein 1 (CIRP-1) 3.5-fold Unchanged N/D 
51-A10 Hypothetical protein 3.5-fold Unchanged Neural 
51-E6 Human, mouse hnRNP-D-like protein 3.5-fold Upregulated Neural 
52-E10 No matches Fivefold Upregulated N/D 
52-G11 Non-receptor protein phosphatase Fourfold Unchanged N/D 
54-B3 βPLC-C/cathepsin-L Sixfold Upregulated Neural 
55-H2 IkB-ϵ Sixfold N/D Neural 
56-G6 Xenopus High-mobility-group (HMG)-X Fourfold Unchanged Published neural 
57-D10 Histone H2A-Z12 Fivefold Upregulated Neural 
57-E10 Clathrin coat adaptor protein complex AP-2 3.5-fold N/D Published neural 
57-G10 TGFβ activating kinase binding protein 3 Fourfold Upregulated Dorsal/Anterior neural 
61-B12 EF1α Fourfold N/D N/D 
61-G10 Microtubule-associated protein Threefold N/D Published neural 
69-F3 No matches Sixfold N/D N/D 
M13-1-G10 PNK-2 Fourfold N/D N/D 
pBS-G7 Activin-Bc Fivefold N/D Published neural 
pBS-G8 Alk5 Fivefold N/D N/D 
CloneIdentityIncrease in arrayRT-PCR analysis*Whole-mount in situ hybridization
28-A12 Cytokeratin- type II Four- to fivefold Downregulated Epidermis 
45-A6 Hypothetical protein. DKFZp586 G1123 Sixfold Upregulated Dorsal-neural 
45-G5 Steroidogenic acute regulatory protein-related (STAR) protein Fourfold N/D N/D 
45-G6 Xenopus cold-inducible RNA-binding protein 2 (CIRP-2) Three- to sevenfold Unchanged Neural 
45-H5 Pro-/Para-thymosin alpha homolog Eightfold Upregulated Neural 
46-E2 FUSE/KH-binding protein Fourfold Upregulated Dorsal-neural 
46-G6 No matches Threefold N/D N/D 
47-A4 CTP synthase II Fourfold Upregulated N/D 
47-B11 Plexin/Semaphorin receptor Fourfold Upregulated Dorsal-neural 
47-F3 No matches Fivefold Unchanged Neural 
47-F5 High-mobility-group (HMG)-like protein Four- to fivefold Upregulated N/D 
47-G3 Human hypothetical protein. Threefold Upregulated Dorsal/anterior neural 
47-G6 DG-42 4.5-fold Downregulated Ventral/epidermal 
47-G10 N-acetyl glucosamine transporter Fourfold N/D N/D 
48-A2 Xenopus tight junction TM-protein; Claudin 3 Fourfold Upregulated Published neural 
48-F11 Hypothetical protein. Fourfold Downregulated Dorsal-neural 
49-B2 Xenopus cold-inducible RNA-binding protein 1 (CIRP-1) 3.5-fold Unchanged N/D 
51-A10 Hypothetical protein 3.5-fold Unchanged Neural 
51-E6 Human, mouse hnRNP-D-like protein 3.5-fold Upregulated Neural 
52-E10 No matches Fivefold Upregulated N/D 
52-G11 Non-receptor protein phosphatase Fourfold Unchanged N/D 
54-B3 βPLC-C/cathepsin-L Sixfold Upregulated Neural 
55-H2 IkB-ϵ Sixfold N/D Neural 
56-G6 Xenopus High-mobility-group (HMG)-X Fourfold Unchanged Published neural 
57-D10 Histone H2A-Z12 Fivefold Upregulated Neural 
57-E10 Clathrin coat adaptor protein complex AP-2 3.5-fold N/D Published neural 
57-G10 TGFβ activating kinase binding protein 3 Fourfold Upregulated Dorsal/Anterior neural 
61-B12 EF1α Fourfold N/D N/D 
61-G10 Microtubule-associated protein Threefold N/D Published neural 
69-F3 No matches Sixfold N/D N/D 
M13-1-G10 PNK-2 Fourfold N/D N/D 
pBS-G7 Activin-Bc Fivefold N/D Published neural 
pBS-G8 Alk5 Fivefold N/D N/D 

The nearest homologs of these clones are listed. Five clones showed no matches in database searches. Four clones have been described in genome-wide sequencing projects as hypothetical proteins. The majority of known clones were full length.

N/D, not determined.

*

RT-PCR analysis performed during neurula stages (stage 15) (see alsoFig. 2 and text for discussion).

Whole-mount in situ hybridization data are based on neurula-stage embryos. Neural implies expression detected in the nervous system, although not necessarily restricted to it (see also Fig. 4).

Genes identified as downregulated genes. All other genes represent upregulated clones identified in the microarray.

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