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Correlate binding sites of two transcription factor from chip-seq data

I have analyzed chip-seq raw data for two TFs oct4 and Nanog. i have a list of the enriched binding sites with their genomic coordinates and also using GREAT i have the gees that fall in these regions along with its TSS coordinates. Please suggest how do i correlate the binding sites of the two transcription factors???

chip-seq tss oct4 association clustering
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updated by Ming Tommy Tang Ming Tommy Tang • written by kamyasingh2490 • kamyasingh2490

are you asking about a correlation of their binding motifs?

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written by TriS TriS

1 answer

you have a peak set of OCT4 and a peak set of Nanog. You can use bedtools intersect to find the how many sites are overlapping each other. If you want a correlation, you may creat a matrix below (1 means the peak is present, 0 means the peak is absent)

               OCT4     Nanog
    peak1      1              1
    peak2      0              1
    peak3      1              0
    peak4      1              1

........

Then calculate the pearson correlation http://stats.stackexchange.com/questions/103801/is-it-meaningful-to-calculate-pearson-or-spearman-correlation-between-two-boolea or use other distance measurement.

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written by Ming Tommy Tang Ming Tommy Tang

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