Genes in open chromatin region
1
0
Entering edit mode
Chris ▴ 10
@3fdb6f97
Last seen 9 days ago
United States

Hi all,

I have a questions about bulk ATAc seq that could not find out myself and also on Biostar. I use Diffbind to get the table below (differential accessibility regions) and then use ChipPeakAnno to annotate the peaks in the P column. Could I conclude that gene with positive Fold (D columns) is more open in diseased than in control (B column vs C column)? Base on the peaks on IGV, could I say this gene in diseased is more chromatin open than the control?Thank you so much!

enter image description here

enter image description here

ChIPpeakAnno DiffBind • 980 views
ADD COMMENT
1
Entering edit mode
@james-w-macdonald-5106
Last seen 27 minutes ago
United States

You have probably not got a response because it looks like you are either joking or trolling. But maybe you are not, so here goes.

You appear to realize that column B is a measure of open chromatin in the diseased samples, and that column C is a measure of the open chromatin in the controls. It's also clear that values of 8 or so are larger than values around 0, and since these are logged data, it's somewhere around 32 256-times larger in disease than control. So yes, the data in your table indicate that there is open chromatin in the diseased samples and probably no open chromatin in your controls.

The other reason it looks like you are trolling is that all of the genes in your table except for that lincRNA are on chrY. The lincRNA is on chr6, but not in the region you are showing.

0
Entering edit mode

Thanks Jame for your help! It is a serious question. Sorry for chosen a bad example so I post a new one. Someone gave me advise that I need to check the value in M column to say if the gene is in open chromatin region.

ADD REPLY
1
Entering edit mode

Well, yes. Ideally you want the open chromatin to be near the TFBS for the gene. Open chromatin that is quite far from any known gene might be difficult to interpret.

ADD REPLY
0
Entering edit mode

So with distance to feature 24 in this case, could I say this gene is more open in diseased than in control? Not sure shortest distance mean, so what is the good distance to safely said a gene is in open chromatin region?

ADD REPLY
1
Entering edit mode

If feature 24 is the single row that is now shown, the answer is yes. But I think you already know that, as I already explained it earlier. As far as a 'good distance', that's a biological question and depends on where the TFBS sites for that particular gene are located.

ADD REPLY
0
Entering edit mode

Thank you for the confirmation! I am still learning ATAC seq. Chatting is not the best way but better than nothing. So if distance to feature like more than +1000 or less than -1000, I could not conclude if the genes are in open chromatin region, is that correct?

ADD REPLY

Login before adding your answer.

Traffic: 742 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6