MEME-ChIP results interpretation

[mdok...@fiu.edu]

Hello,

I am analyzing ChIP-Seq data from Illumina using Galaxy web server. I mapped the reads with bowtie2 tool and did the peak calling with MACS2. The next thing I did is to annotate the peaks with genomic regions i.e. promoter, intergenic, intron etc and gene names. The output looks like picture below-

After this, I have used the peak region coordinates to convert into fasta format. Then, I used the Fasta format file of these peak regions to analyze and discover significant motifs with the help of MEMEChIP tool.  I have got the following file

Now my question is that the 4th column-  Known or Similar Motifs represents gene names are transcription factor binding to particular motif or genes consists of these particular significant motifs?

[CharlesEGrant]

Motifs are usually named for the transcription factor which binds to that motif, but in some cases the motif was known before the TF was known. You should follow the links to the identified motif, and study any provided information. You have to be very careful about accepting “Known or Similar Motifs” at face value. Tomtom is simply saying that the similarity between the observed motif and the known motifs is statistically significant. This is not a guarantee that the observed motifs is an instance of the known motif. You should manually confirm that the match makes biological sense. This may require studying the literature for the identified TF.

In the results you attached it looks like your sequences contain simple repeats and low complexity regions. Motifs like TCTCTCTC… or GGGGGGG… are unlikely to be biologically relevant. You may want to screen your sequences for low complexity regions and simple repeats before analyzing them with MEME-ChIP. Tools like DUST (included with the MEME Suite source), TRF, and Repeat-Masker are often used for this purpose.