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    SourceForge net ctcf chip exo
    ( A ) Size distribution of border pairs called by MACE (purple) and by Rhee et al . (2011) (green). MACE border pair had a single mode (centered at 49), whereas border pairs identified by Rhee et al . had bimodal distribution (centered at 13 and 49). ( B ) <t>CTCF</t> <t>ChIP-exo</t> raw sequencing tags density profile around predicted CTCF motifs. The blue and red curve indicates the tag density profile calculated from reads mapped to the forward and reverse strand, respectively. Bimodal patterns were observed for forward and reverse signals.
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    ( A ) Size distribution of border pairs called by MACE (purple) and by Rhee et al . (2011) (green). MACE border pair had a single mode (centered at 49), whereas border pairs identified by Rhee et al . had bimodal distribution (centered at 13 and 49). ( B ) CTCF ChIP-exo raw sequencing tags density profile around predicted CTCF motifs. The blue and red curve indicates the tag density profile calculated from reads mapped to the forward and reverse strand, respectively. Bimodal patterns were observed for forward and reverse signals.

    Journal: Nucleic Acids Research

    Article Title: MACE: model based analysis of ChIP-exo

    doi: 10.1093/nar/gku846

    Figure Lengend Snippet: ( A ) Size distribution of border pairs called by MACE (purple) and by Rhee et al . (2011) (green). MACE border pair had a single mode (centered at 49), whereas border pairs identified by Rhee et al . had bimodal distribution (centered at 13 and 49). ( B ) CTCF ChIP-exo raw sequencing tags density profile around predicted CTCF motifs. The blue and red curve indicates the tag density profile calculated from reads mapped to the forward and reverse strand, respectively. Bimodal patterns were observed for forward and reverse signals.

    Article Snippet: AVAILABILITY Raw and processed data of CTCF ChIP-exo, source code and documentation of MACE are available at http://chipexo.sourceforge.net/ .

    Techniques: Chromatin Immunoprecipitation, Sequencing

    Comparing MACE with the method used by Rhee et al . (2011). ( A ) Bar-plot showing percent of putative binding regions (green areas) supported by CTCF canonical motif (RSYDMCMYCTRSTGK). The bar height indicates the number of total binding regions (exact numbers are superimposed on top). (B) Bar-plot showing percent of putative binding regions (red area) cross-validated by ENCODE CTCF ChIP-seq. ( C ) Comparing average conservation score (PhastCon) between regions identified by MACE and Rhee 2011. All binding regions identified by the two methods were combined and then divided into three groups: common border pair (black), MACE-unique (red) and Rhee et al .-unique (blue). ( D ) Cumulative curves used to compare spatial resolution between MACE and Rhee 2011. CTCF indicates CCCTC binding factor; MACE, model-based analysis of ChIP-exo.

    Journal: Nucleic Acids Research

    Article Title: MACE: model based analysis of ChIP-exo

    doi: 10.1093/nar/gku846

    Figure Lengend Snippet: Comparing MACE with the method used by Rhee et al . (2011). ( A ) Bar-plot showing percent of putative binding regions (green areas) supported by CTCF canonical motif (RSYDMCMYCTRSTGK). The bar height indicates the number of total binding regions (exact numbers are superimposed on top). (B) Bar-plot showing percent of putative binding regions (red area) cross-validated by ENCODE CTCF ChIP-seq. ( C ) Comparing average conservation score (PhastCon) between regions identified by MACE and Rhee 2011. All binding regions identified by the two methods were combined and then divided into three groups: common border pair (black), MACE-unique (red) and Rhee et al .-unique (blue). ( D ) Cumulative curves used to compare spatial resolution between MACE and Rhee 2011. CTCF indicates CCCTC binding factor; MACE, model-based analysis of ChIP-exo.

    Article Snippet: AVAILABILITY Raw and processed data of CTCF ChIP-exo, source code and documentation of MACE are available at http://chipexo.sourceforge.net/ .

    Techniques: Binding Assay, Chromatin Immunoprecipitation