Additional file 1:

Supplementary Notes. This is a word document describing and demonstrating the hypothesis test for classifier accuracy. Also described are the possible roles of WT1 in nervous tissue development and cellular migration. The hypothetical relationship between WT1 and the Wnt pathway are also discussed.

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Additional file 2:

This file contains several sub-folders. The folder "Classifier Results" contains the SVM predictions for all TFs in this study as well as a list of classifiers and their associated performance measures. The new predictions for all TFs are also available for query and download on our website[30]. The folder "Literature_curated_targets" contains the known TF-target interactions taken from databases and the literature. Any interactions manually curated from primary literature are listed, and the Pubmed ID of the article used is given. All files are annotated so as to be self explainatory or have an accompanying Readme file.

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Additional file 3:

This file contains two excel spreadsheets providing the functional annotations of known targets and predicted targets of OCT4 respectively. These are annotations as provided by the DAVID system at NIH and include the statistical significance of each functional category.

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Additional file 4:

Using both known and newly predicted targets, this file contains a list of genes which relate to apoptosis as given by the DAVID functional analysis tools. The genes appear several times in various, similar annotation categories which are related to cell death pathways.

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Additional file 5:

Using just the newly predicted targets, this file contains a list of genes which relate to cellular adhesion, cytoskeleton, or motility as given by the DAVID functional analysis tools.

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Additional file 6:

Using both known and newly predicted targets, this file contains a list of genes which are annotated to terms by DAVID which are somehow related to the nervous system. Three main categories are present (represented by folders) which each contain several functional terms and the genes annotated to them. The three main categories are "Neuron related", "Sensory perception", and "Voltage gated channels and membrane receptors".

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Additional file 7:

Using both known and newly predicted targets, this file contains a list of genes and the chromosomal cytobands to which they are mapped. p-values generated by DAVID are also given to show statistical enrichment.

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Additional file 8:

This file contains the results of running the Weeder algorithm on 1) the set of known and newly predicted (Platt score P ≥ 0.95) targets of WT1, and 2) the known targets of WT1. Sequence regions used are as defined in Methods. The file also contains the results of Oligo-analysis. Also included are the matching results after scanning the literature derived consensus sites for WT1 against the full set of WT1 targets (predicted and known).

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