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Open Access Methodology article

Finding combinatorial histone code by semi-supervised biclustering

Li Teng1 and Kai Tan12*

Author Affiliations

1 Department of Internal Medicine, University of Iowa, Iowa City, IA, USA

2 Department of Biomedical Engineering, University of Iowa, Iowa City, IA, USA

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BMC Genomics 2012, 13:301  doi:10.1186/1471-2164-13-301

Published: 3 July 2012

Additional files

Additional file 1:

Table S1. List of 362 combinatorial histone modifications identified by tandem mass spectrometry [14-17]. Table S2. Number and fraction of distal p300 peaks that have only one histone modification peak. Table S3. Overlap between B cell enhancers from the biclusters in this study and those reported in Ernst et al. [20]. Table S4. Overlap between ES cell enhancers from the biclusters in this study and those reported in Ernst et al. [20]. Table S5. Overlap between enhancer biclusters that have more H3K4me1 mark and PReMod cis-regulatory modules.

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Additional file 2:

Figure S1. Venn diagram of enhancers in three cell types used as inputs to the biclustering algorithms. Figure S3. Promoter coverage of all 26 possible histone states involving at least two histone modification marks.

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Additional file 3:

Table S6. Histone states of enhancers as defined by biclustering in B, T, and ES cells.

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Additional file 4:

Table S7. Gene ontology term enrichment among genes located near two classes of enhancers in ES cells.

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Additional file 5:

Figure S2. Pseudo code for the semi-supervised CoSBI algorithm.

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