I have up and down-regulated genes from bulk RNA result from DeSeq2. Genes that are differential in chromatin accessibility between two conditions from DiffBind. I would like to find the genes overlap between bulk RNA and ATAC-seq assay as these papers but don't know the code to get it. Would you please have a suggestion? Thank you so much 😃.
in silico DEG details I used intersect function in R which can do the same job. Which I am not sure is the experiment try to find transcription factors that cause the difference in phenotype between 2 conditions. DEG in bulk-RNA from DeSeq2 (log2 fold change >2.5 or log2 fold change < -2.5) intersect with genes differently in chromatin accessibility from DiffBind (log2 fold change >2.5 or log2 fold change < -2.5). I narrowed down to 142 genes.
For atac-seq result, after applying filter log2fold > 2.5 or log2fold < -2.5 and p value < 0.00001, I still got around 12k genes that are different between 2 conditions. Meanwhile bulk-RNA after apply filter has only around 300 genes. The number of genes in human and pig are similar so I am not sure about the number of gene I have in atac-seq
What do you think about this approach because I don't use MEME or TOMTOM?
I share with you what the author did.
" In order to screen new transcription factors by combining with star transcription factors. First, we used MEME software to predict the motif of Duroc pigs' peaks. Second, we compared the transcription factor database with TOMTOM to predict all transcription factors that may bind to the chromatin open regions . Third, we found all possible binding sites of MYOD, MYOG, MYF5, MYF6 and MEF2 families and did a union. A total of 99 sites were found. "Fourthly, we counted other transcription factors that may bind to these 99 sites and sorted them by the number of binding sites. All of the above statistics were manually counted."
Will read more to give you a good reply. Thank you so much 😃