Open Access Research article

Overrepresentation of transcription factor families in the genesets underlying breast cancer subtypes

Himanshu Joshi12, Silje H Nord3, Arnoldo Frigessi4, Anne-Lise Børresen-Dale23 and Vessela N Kristensen123*

Author Affiliations

1 Department of Clinical Molecular Biology and Laboratory Sciences (EpiGen), Division of Medicine, Akershus University Hospital, Lorenskog, Norway

2 Institute for Clinical Medicine, University in Oslo, Oslo, Norway

3 Department of Genetics, Institute for Cancer Research Oslo University Hospital, Radiumhospitalet, Norway

4 Department of Biostatistics, Institute of Basic Medical Sciences, University of Oslo, Blindern, 0317, Oslo, Norway

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BMC Genomics 2012, 13:199  doi:10.1186/1471-2164-13-199

Published: 22 May 2012

Additional files

Additional file 1:

Table S1. Subtype-specific gene list. Table shows the 197 subtype-specific best discriminatory genes, which is a subset of the intrinsic gene-list.

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Additional file 2:

Figure S1. Histogram of z-scores of overrepresentation. Histogram of TFBS matrix family overrepresentation observed in subtype-specific promoters compared to the reference genomic promoter background shown as z-scores.

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Additional file 3:

Figure S2. Direct interactions between genes defining subtypes. Subtype-relevant key driver interactions for Luminal A, B and ERBB2+ subtypes.

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Additional file 4:

Figure S3. Protein-protein interactions and TF interactions associated with Luminal A subtype. Network shown here is based on the luminal A specific genelist.

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Additional file 5:

Figure S4. Protein-protein interactions and TF interactions associated with Luminal B subtype. Network shown here is based on the luminal B specific genelist.

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Additional file 6:

Figure S5. Protein-protein interactions and TF interactions associated with ERBB2+ subtype. Network shown here is based on the ERBB2+ subtype-specific genelist.

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Additional file 7:

Figure S6. Protein-protein interactions and TF interactions associated with basal subtype. Network shown here is based on the basal subtype-specific genelist.

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Additional file 8:

Figure S7. Protein-protein interactions and TF interactions associated with normal-like subtype. Network shown here is based on the normal-like subtype-specific genelist.

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Additional file 9:

Table S2. TFBS overrepresentation in subtypes-specific gene promoters. List of significantly over-represented transcription factor binding site families in subtypes of breast cancers at the cut-off level of z- score > =2.0.

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Additional file 10:

Table S3. Over-representation of potential TFBS in subtype-specific promoter sequences. Table shows the fold over-representation of potential transcriptional factor hits (represented as TFBS families) in subtype- specific gene promoter sequences.

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Additional file 11:

Table S4. Correlation between TFBS overrepresentation and mRNA expression of corresponding TF genes. Table displays the Pearson’s correlation between the geometric mean of expression values of transcription factor genes in subtypes and fold overrepresentation of corresponding TFBS families.

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