Re: Re: Fwd: genome - soe.ucsc.edu admins: Message Pending [{IPnW7szAyunJdioCb2kwAgYuZGPZ7oKr0}]

[Maximilian Haeussler]

Hi Zou,

yes, go to Tools > Table Browser, select the human genome, assembly hg38, select under Group = "Regulation", then select the track "JASPAR"  Transcription Factors, as in the screenshot below:

Then you can either enter a single region to export, e.g. chr4:110,617,423-110,623,077 under "Define regions of interest > position.

 

Or you can enter multiple regions, e.g. "chr4 110617423 110623077", one per line, when you click on "Define regions"

At the bottom of the page you can then download the JASPAR data by selecting output format = "BED" and clicking "get output"

Hope this helps and let us know if you have any other questions,

best

Max

On Mon, Jan 29, 2024 at 9:40 AM Zou Jiawen <zou...@zju.edu.cn> wrote:

   

        I tried to use JASPAR_familial_hub, and it seems that I can get the desired results, but there is a

problem. Although I click on each transcription factor to get detailed information including its score,

is there a way to download the data of predicted transcription factors including score? After all, I

have a series of genes that I want to query, and the manual method is too slow.

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                                      Zou JW

                                      2024/1/29

-----原始邮件-----
发件人: "Maximilian Haeussler" <mhae...@ucsc.edu>
发送时间: 2024-01-26 21:50:55 (星期五)
收件人: "Zou Jiawen" <zou...@zju.edu.cn>
主题: Re: Fwd: genome - soe.ucsc.edu admins: Message Pending [{IPnW7szAyunJdioCb2kwAgYuZGPZ7oKr0}]

Did you try to use the track JASPAR on the UCSC genome browser directly? You don't need the JASPAR web page. The track exists on hg38 and hg19 at least.

On Fri, Jan 26, 2024 at 2:50 PM Zou Jiawen <zou...@zju.edu.cn> wrote:

Hi, first of all thank you for your replies.

Now I have a list of genes and want to predict the transcription factors that regulate these genes, but I didn't find the corresponding tool on the JASPAR web page

---

                                      Zou JW

                                      2024/1/26

-----原始邮件-----
发件人: "Maximilian Haeussler" <mhae...@ucsc.edu>
发送时间: 2024-01-26 16:49:02 (星期五)
收件人: zou...@zju.edu.cn, "Browser QA" <brows...@soe.ucsc.edu>
主题: Fwd: genome - soe.ucsc.edu admins: Message Pending [{IPnW7szAyunJdioCb2kwAgYuZGPZ7oKr0}]

Hi Jiawen,

the JASPAR webserver seems to be down which is unfortunately not something we can fix on our side, you'd have to alert the JASPAR developers.

But: Can you let us know why you can't use the "JASPAR" native track on hg38 and hg19? 

best

Max

---------- Forwarded message ---------
From: UCSC Genome Browser Public Support <genome+...@soe.ucsc.edu>
Date: Fri, Jan 26, 2024 at 3:26 AM
Subject: genome - soe.ucsc.edu admins: Message Pending [{IPnW7szAyunJdioCb2kwAgYuZGPZ7oKr0}]
To:

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---------- Forwarded message ----------
From: Zou Jiawen <zou...@zju.edu.cn>
To: gen...@soe.ucsc.edu
Cc: 
Bcc: 
Date: Fri, 26 Jan 2024 10:26:25 +0800 (GMT+08:00)
Subject: How to connect to public hubs JASPAR TFBS

Dear UCSC developer

 

       I am currently hoping to utilize UCSC to query multiple gene sequences for potentially bound transcription factors, but when I try to connect to the JASPAR TFBS hubs the following error is displayed:

        ERROR: TCP non-blocking connect() to expdata.cmmt.ubc.ca IP 137.82.44.19 timed-out in select() after 10000 milliseconds. 

A connection timeout means that either the server is offline or its firewall, the UCSC firewall or any router between the 

two blocks the connection. Couldn't open http://expdata.cmmt.ubc.ca/JASPAR/UCSC_tracks/hub.txt.

      

     I don't know how to solve it at the moment. I look forward to your reply. Thank you.

---

                                      Zou JW

                                      2024/1/26