conservative analysis

[Jiarui Mi]

Hi, 

I am doing conservative analysis across different specious on UCSC website. Basically we want to identify conservative cis-regulatory elements in zebrafish genome and clone the tissue specific enhancers. I tried to search the gene name first using mouse genome (mm10) and what I can see are different bars which suggesting conservative regions. My question is what are the meanings of the color of these bars? And is it possible that I can fetch the conservative sequence directly from zebrafish genome rather than from the mouse ones? Thanks!

Best/

Jiarui

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[Matthew Speir]

Hello, Jiarui. 

Thank you for your question about conservation data in the UCSC Genome Browser. 

It's not clear what bars you are referring to in your email, but I have annotated your image and labeled the different tracks with what type of data they are:

The tracks boxed in red are gene tracks, the one boxed in orange is a track of expression data, the one boxed in blue is per-base conservation calculated across placental mammals (there are different tracks for other vertebrate groups), and the one boxed in black is a multiple alignment showing a handful of vertebrate species aligned to mouse (only a subset are shown by default, more can be activated form the track controls).

If you are looking at a region in one genome assembly (e.g. mouse mm10), you can try to view this region in another assembly using the option "In Other Genomes (Convert)" option under the "View" menu. Note that the genome assemblies available will vary as it depends on us having created a pairwise alignment between the two assemblies. 

Additionally, you may be interested in a few of the Zebrafish public track hubs available: http://genome.ucsc.edu/cgi-bin/hgHubConnect?hubSearchTerms=&hgHub_do_search=on&hubDbFilter=danRer11, specifically the "DANIO-CODE Track Hub", "JASPAR TFBS", and "ZebrafishGenomics" hubs. To view the data for one of these hubs, click the connect button and then navigate to the Zebrafish/danRer11 assembly. You can connect more hubs by navigating back to the public hub list via the "My Data > Track Hubs" menu at the top of the page. 

Lastly, there are also a handful of Comparative Genomics tracks available for the Zebrafish/danRer11 assembly that may be of interest to you. We provide three pairwise alignment chain/net tracks:

• danRer11 and human hg38: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=danRer11&g=chainNetHg38
  
• danRer11 and mouse mm10: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=danRer11&g=chainNetMm10
  
• danRer11 and chicken galGal6: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=danRer11&g=chainNetGalGal6

Here's a session where you can see all three of these tracks plus a selection of tracks from the three public hubs I mentioned earlier: http://genome.ucsc.edu/s/mspeir/danRer11_mlq_conservation. To learn more about and configure 

the different tracks, you can navigate to their description pages through the grey bar next to the track items on the left side of screen or through the track name below the genome browser image (e.g. "JASPAR2020 TFBS danRer11"). 

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Training videos & resources: http://genome.ucsc.edu/training/index.html

Want to share the Browser with colleagues? Host a workshop: http://bit.ly/ucscTraining

---

Matthew Speir

UCSC Cell Browser, Quality Assurance and Data Wrangler

Human Cell Atlas, User Experience Researcher

UCSC Genome Browser, User Support

UC Santa Cruz Genomics Institute

Revealing life’s code.

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[Jiarui Mi]

Hi, 

We got some nice explanantion from Matthew Speir and the tracks he suggested are quite helpful. We have some further questions about cross species analysis. Basically we are interested in getting conservative cis-regulatory element in zebrafish and tried to clone them into our vector. We noticed that there are quite many score systems available to evaluate the conservative ratio but I can hardly fetch the data from UCSC (also it would be good if you can help explain a little bit about the the score systems you have). 

For example, we found in one paper (attached here) showing that there is a tissue specific enhancer region in tp63 intron 3 regions which is very conservative between mouse and zebrafish. Can we make the same conclusion based on the tracks available in UCSC? For this type of conservative analysis, what analytical pipeline you recommend. 

Thank you very much for your attention and very looking forward to your reply!

Best

Jiarui

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发件人: Matthew Speir <msp...@ucsc.edu>
发送时间: 2020年8月8日 0:09
收件人: Jiarui Mi <jiar...@ki.se>
抄送: gen...@soe.ucsc.edu <gen...@soe.ucsc.edu>
主题: Re: [genome] conservative analysis

 

[Luis Nassar]

Hello Jiarui,

We have limited conservation data on zebrafish. On the latest assembly (danRer11) we only offer the chain nets to other organisms. However, danRer11 does have multiple Public Hubs (http://genome.ucsc.edu/cgi-bin/hgHubConnect). These hubs are data available for the assembly generated and hosted by outside groups. These include:

• JASPAR TFBS
• DANIO-CODE
• Zebrafish Genomics (from Burgess lab)

These hubs offer transcription factor, expression, and conservation data. More specifically, the ZebrafishGenomics hub offers phastCons data from genomic 4-way comparison (zebrafish, grass carp, common carp and goldfish).

Here is a session (http://genome.ucsc.edu/s/Lou/danRer11Cons) looking at the third intron of tp63. The bottom two data tracks represent the phastCons data. One is a signal track, and the second a discreet conserved elements track. You can click on the tracks for more information. This data can be obtained through the Table Browser (http://genome.ucsc.edu/cgi-bin/hgTables). The session also includes data tracks from the other danRer11 hubs.

If you have any questions on the hub data, these should be directed to the providers. These contacts can be found in the credits section of the track description pages.

Let us know if you have any further questions we can help with.

Please include gen...@soe.ucsc.edu in any replies to ensure visibility by the team. All messages sent to that address are archived on our public forum. If your question includes sensitive information, you may send it instead to genom...@soe.ucsc.edu.

Lou Nassar
UCSC Genomics Institute

To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/VI1PR08MB5310B9AA0EA06F0BBB9DA6ACE6460%40VI1PR08MB5310.eurprd08.prod.outlook.com.