Re: efficiency?
Shiaoching Gong
Thanks Max.
Yes, I can not find transcription factors for mouse genes. I checked several links, but did not not.
Best,
Shiaoching
From: Maximilian Haeussler <mhae...@ucsc.edu>
Sent: Thursday, August 13, 2020 9:16 AM
To: Shiaoching Gong <shg...@med.cornell.edu>
Subject: [EXTERNAL] Re: efficiency?
did you ask gen...@soe.ucsc.edu ? Sorry somehow didn't reply to your email earlier, I was off for two weeks.
On Wed, Jul 29, 2020 at 12:03 AM Shiaoching Gong <shg...@med.cornell.edu> wrote:
HI Max,
Is it possible to find transcription factors for mouse Ch25h gene? I found human in year of 2009, but cound not find for mouse.
Thanks,
Shiaoching
From: Shiaoching Gong
Sent: Tuesday, July 28, 2020 5:40 PM
To: 'Maximilian Haeussler' <m...@soe.ucsc.edu>
Subject: RE: [EXTERNAL] Re: efficiency?
Thanks Max.
I was searching for transcription factors for Ch25h gene and found only year of 2009 has this function. Could you please let me know if other years have this function? I also have a question about the number at the end of each transcription factor.
For example EZH2, 2/14
FOXP2, ½
CTCF, 15/99
What does the number mean?
Thanks,
Shiaoching
From: Maximilian Haeussler <m...@soe.ucsc.edu>
Sent: Thursday, December 19, 2019 4:18 PM
To: Shiaoching Gong <shg...@med.cornell.edu>
Subject: [EXTERNAL] Re: efficiency?
This is a good question. If you’re not interested in variants, you could use hg19 or hg38. Hg38 is the current version and supposedly “better”.
I should have documentation about this, too...
On Thu 19 Dec 2019 at 22:12, Shiaoching Gong <shg...@med.cornell.edu> wrote:
Good afternoon Max.
There are four options to select human DNA. I am not sure which one to select. Could you please advise?
Thanks,
Shiaoching
From: Maximilian Haeussler <m...@soe.ucsc.edu>
Sent: Tuesday, December 17, 2019 8:47 AM
To: Shiaoching Gong <shg...@med.cornell.edu>
Subject: [EXTERNAL] Re: efficiency?
In the target genome hg19, there is no exact match to your sequence:
You can check it here http://genome.ucsc.edu/cgi-bin/hgBlat
The best match has a 1bp mismatch. Click on details to show it.
Where did you find this sequence? Not in the official reference genome...
On Mon, Dec 16, 2019 at 8:52 PM Shiaoching Gong <shg...@med.cornell.edu> wrote:
Dear Max,
Thank you for your prompt reply and help. I really appreciate it.
Here is the link, I just donot know why I can not get a real number for efficiency.
http://crispor.tefor.net/crispor.py?batchId=Mm6TRoDEaWFQoGfMGiVD
Best,
Shiaoching
From: Maximilian Haeussler <m...@soe.ucsc.edu>
Sent: Monday, December 16, 2019 1:41 PM
To: Shiaoching Gong <shg...@med.cornell.edu>
Subject: [EXTERNAL] Re: efficiency?
Can you send me the link of this page? I need to know about more about the rest of the page ...
On Mon 16 Dec 2019 at 18:22, Shiaoching Gong <shg...@med.cornell.edu> wrote:
Dear Sir/Madam,
Could you please let me know what does the following data mean? I do not see the cutting efficiency, they only show – and –
93, 96 and – ? and –?
Could you please advise?
Thanks very much,
Shiaoching
Brian Lee
Thank you for using the UCSC Genome Browser and your question about Transcription Factor data for the mouse gene CH25H.
You may be interested in the Public Hubs on mm10 that have some TFBS data such as the JASPAR Hub connected and displayed in his session: http://genome.ucsc.edu/s/brianlee/mm10_Ch25h
Questions about the JASPAR tracks should be directed to the source of the data with further resources here: http://jaspar.genereg.net/genome-tracks/
To address the question about the numbers next to the blocks on the human hg19 gene CH25H seen in this session at the top: http://genome.ucsc.edu/s/brianlee/hg19_Ch25h
EZH2, 2/14
FOXP2 1/2
CTCF, 15/99
In this case the 2/14 for the Transcription Factor EZH2 refers to the cell count(detected/assayed) for evidence of this factor binding on this location. If you click into EZH2 block you will see the two cellTypes (GM12878 and NH-A) where evidence from experiments indicated a hit. If you expand the section titled "Assays for EZH2 Without Hits in Cluster" you will see 12 other cellTypes where the experiments did not indicate evidence, which may or may not be of interest. Likewise, if you click the CTCF, 15/99 block you will see the 15 tissues what clustered with indications of a binding spot. By expanding othe other without hits section you will see the remaining 84 experiments (99-15=84) that did not show evidence of these hits.
If you click the "Go to Txn Factor ChIP track controls" link on the details pages for items you can find controls that allow you to turn these pieces of information on or off in the general browser view if they are not of interest: Cluster right label: [x] cell count (detected/assayed)
With this session view link above you can jump to the mouse genome by going to the top "View" menu and selecting "In Other Genomes" and then selecting the dropdown choice of mouse and then move the default from mm10 to mm9 and click Submit. For this session view you will then be brought to the mouse coordinates of chr19:34548270-34549676 with "(98.2% of bases, 100.0% of span)" mapping information noted. If you go down to the blue bar group title "Expression and Regulation" you will see many groups of tracks with "TFBS" next to the name that you can turn on (Caltech TFBS, PSU TFBS, LICR TFBS, Stan/Yale TFBS). Each lab group did experiments on a different number of factors on different cell lines. You could turn on just one, such as the Stan/Yale TFBS track and put on only the MEL cell line and and set only the Peaks to pack and hide the Signal track. The result would be this view: http://genome.ucsc.edu/s/brianlee/mm9_Ch25h
This data shared on mm9 dates back to 2012 when we did not build a clustered TFBS track on mouse similar to the one on human originally referenced since there was not as wide a number of experiments as done in human. You may be able to find more updated resources for mouse transcription factors at one of these unaffiliated sites, FactorBook and ENCODE which have compiled TFBS experiment data.
https://factorbook.org/
https://www.encodeproject.org/search/?type=Experiment&related_series.%40type=ReferenceEpigenome&assay_title=TF+ChIP-seq&replicates.library.biosample.donor.organism.scientific_name=Mus+musculus
If you have any more questions, please reply-all to gen...@soe.ucsc.edu. All messages sent to that address are publicly archived. If your question includes sensitive data, please reply-all to genom...@soe.ucsc.edu.
All the best,
Brian Lee
--
---
You received this message because you are subscribed to the Google Groups "UCSC Genome Browser Public Support" group.
To unsubscribe from this group and stop receiving emails from it, send an email to genome+un...@soe.ucsc.edu.
To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/BL0PR06MB47889208FCA0F937C530479AEE430%40BL0PR06MB4788.namprd06.prod.outlook.com.