Additional File 1:

Supplementary scatter plots. (A-F) Shows scatter plot comparisons of the conditions not shown in Figure 2. Log₂-expression values were averaged between replicates and then plotted against the mean log₂-expression of the stage-matched Ven condition. (A) Nog vs Ven, stage 10. (B) Dkk vs Ven, stage 10. (C) Nog vs Ven, stage 11.5. (D) Nog+Dkk vs Ven, stage 11.5. (E) Dkk vs Ven, stage 11.5. (F) Dor vs Ven, stage 11.5. Probe sets measuring two known organizer genes, otx2 (green) and gsc (red), are labeled within the plots (otx2 probe sets: Xl.1268.1.S1_at, Xl.3004.1.A1_at, Xl.11672.1.A1_at, and XlAffx.1.11.S1_at; gsc probe sets: Xl.801.1.A1_at, Xl.801.1.S1_at, and Xl.801.1.S1_s_at). (G-I) Shows scatter comparisons of selected single arrays, further illustrating the relative amounts of clutch variation and experimental variation. (G) Dkk vs Ven, clutch 3 stage 11.5. (H) Dor vs Ven, clutch 3 stage 11.5. (I) Ven clutch 3 vs Ven clutch 4, stage 11.5. Note that the R-square value in (I) is less than (G) and (H), showing greater clutch variation than experimental variation.

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Additional File 2:

Genes regulated by ectopic organizer signaling. This tab delimited table contains information about the all of the genes which passed at least one RP method test above the 10% FDR cutoff in the Nog, Nog+Dkk, or Dkk conditions, when compared to Ven, at either stage. Figure 3 shows the results of hierarchical clustering of this list; genes are listed in the same order as the cluster. Columns: List Number, Affymetrix Probe Set, Unigene ID, Gene Title, Gene Symbol. Names and symbols were assigned by the Affymetrix NetAffx database [64].

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Additional File 3:

Genes that show similar regulation in the full organizer conditions. This tab delimited table contains information about the genes selected for our second list. Each gene was required to show either up-regulation or down-regulation that attained a RP test score less than 0.0006 in both the Nog+Dkk and Dor conditions, when compared to Ven. Genes are listed in the same order as the hierarchical cluster shown in Figure 7. Columns: List Number, Affymetrix Probe Set, Unigene ID, Gene Title, Gene Symbol. Names and symbols were assigned by the Affymetrix NetAffx database [64].

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Additional File 4:

GO Biological Process annotation of the Xenopus laevis genome. This tab delimited table contains the machine-generated GO Biological Process annotation used in this paper. Columns: Affymetrix Probe Set, Confidence Value, Biological Process ID, Biological Process Term.

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Additional File 5:

Precision and accuracy of the GO Biological Process annotation. The accuracy and precision of the annotation test data are plotted against the number of votes. See Vinayagam et al. [48] for a description of the method used to produce these measures.

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