Open Access Research article

Genome-wide identification of new Wnt/β-catenin target genes in the human genome using CART method

Christian Hödar1*†, Rodrigo Assar2†, Marcela Colombres4†, Andrés Aravena2, Leonardo Pavez1, Mauricio González1,2, Servet Martínez2,3, Nibaldo C Inestrosa4 and Alejandro Maass2,3

  • * Corresponding author: Christian Hödar chodar@inta.cl

  • † Equal contributors

1 Laboratorio de Bioinformática y Expresión Génica, INTA, Universidad de Chile, Santiago, Chile

2 Laboratorio de Bioinformática y Matemática del Genoma, Centro de Modelamiento Matemático (UMI 2807, CNRS), Facultad de Ciencias Físicas y Matemáticas, Universidad de Chile, Santiago, 8370459, Chile

3 Departamento de Ingeniería Matemática, Facultad de Ciencias Físicas y Matemáticas, Universidad de Chile, Santiago, 8370459, Chile

4 Centro de Regulación Celular y Patología "Joaquín V. Luco" (CRCP), MIFAB, Facultad de Ciencias Biológicas, Departamento de Biología Celular y Molecular, Pontificia Universidad Católica de Chile, Santiago, 8330025, Chile

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BMC Genomics 2010, 11:348 doi:10.1186/1471-2164-11-348

Published: 1 June 2010

Additional files

Additional file 1:

New proposed Wnt/β-catenin canonical pathway target genes selected by multiple CART method. The file contains the list of 15,476 genes classified by the different methods discussed in the text. In particular the 89 new Wnt/β-catenin targets predicted by our method and the 66 known genes used in the training procedure.

Format: XLSX Size: 2.4MB Download file

Open Data

Additional file 2:

Ranking of the variables used by the proposed method. The file contains for each one of the 432 TF binding site motif its ranking according to: frequency of use and index I1 as described in the text.

Format: XLSX Size: 63KB Download file

Open Data

Additional file 3:

Gene ontology analysis of known and proposed Wnt/β-catenin pathway target genes. The file contains the GO analysis count performed on known and predicted Wnt/β-catenin targets.

Format: XLS Size: 39KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 4:

Gene ontology terms for proposed Wnt/β-catenin pathway target genes. The file contains the complete GO terms for the predicted Wnt/β-catenin pathway target genes.

Format: TXT Size: 53KB Download file

Open Data

Additional file 5:

Cluster of gene expression for proposed Wnt/β-catenin pathway target genes. The file contains the heat map results from cluster analysis using data from BioGPS database.

Format: PPT Size: 2.9MB Download file

This file can be viewed with: Microsoft PowerPoint Viewer

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Additional file 6:

Human footprinting matrix used in the CART procedure. The file contains the original data file obtained from [86], the code used to transform them to files "genes.txt", "motifs.txt" and "upstream.txt", and the code used to load them to R data format. File "upstream.txt" contains a text plain matrix with genes in rows and predicted transcription factor binding site motifs in columns, adopting the value 0 when no TF binding site motif is predicted or the number of TF binding site motifs predicted by PRIMA.

Format: ZIP Size: 11.5MB Download file

Open Data

Additional file 7:

Function codes and routines implemented in R for the CART procedure. The file contains the files used in CART procedure: onetree.R is used to train a single tree, consolide.R is used to summarize the 1,500 trees to obtain the gene score and rankvars.R is used to determine the score of the variables (TF binding sites motifs). Finally, Makefile is used to coordinate all computations using GNU make.

Format: ZIP Size: 3KB Download file

Open Data