genome and others

[loubna el - zein]

Dear,

I would like to know how to use your data in order to compare between cow and human genome or transcripts as well as their up and downstream flanking regions, and how to use cow genome as well as that of human?

thank you in advance

regards

Loubna EL ZEIN, PhD
--------------------------------------

 Associate Professor

Lebanese University - Faculty of Sciences I

Biology department

Rafic Hariri Campus - Po. Box: 14 – 6573

Hadath- Beirut – Lebanon

Cell phone : 00961 3 751271

[loubna el - zein]

dear,

How to find diseases that are linked to gene variants in human and cows?

[Daniel Schmelter]

Hello Loubna,

Thank you for using the Genome Browser and for writing in with your question about comparing human and cow genome data.

We have a few resources that link human and cow genome data, depending on your use case. We cannot advise you on how to make conclusions about specific diseases or comment on your analysis pipeline since this email is intended only to support Genome Browser tools.

Starting with the cow genome, the UCSC Genome Browser has the full, updated set of NCBI RefSeq genes for the latest cow reference genome, bosTau9. Both of these can be accessed from the cow genome below, but are usually better when you are looking at a specific region. On bosTau7, you can find the dbSNP138 variant annotation and the QTL track which has cattle trait-genome associations from the Cattle QTLdb.

https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=bosTau9&g=refSeqComposite
https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=bosTau7&g=snp138
https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=bosTau7&g=animalQtl
https://www.animalgenome.org/cgi-bin/QTLdb/BT/ontrait?trait_ID=1464

From the human genome, there are a myriad of disease and variant datasets. Some of our most popular are dbSNP153, ClinVar Variants, and OMIM Variants. We encourage you to look at the whole list in the "Variants" section and the "Phenotype and Literature" section.

https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=dbsnp153
https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=clinvar
https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=omimAvSnp

To connect the two genomes, we recommend the LiftOver and BLAT tools. LiftOver takes lists of coordinates from one organism (human) and maps them onto another organism (cow). This may be useful alongside BLAT, which aligns sequences to a particular genome and shows more imperfect matches. The cow genomes also have an alignment track that maps the human genome onto the cow, the Chains and Nets conservation tracks.

https://genome.ucsc.edu/cgi-bin/hgLiftOver
https://genome.ucsc.edu/cgi-bin/hgBlat
https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=bosTau9&g=chainNetHg38

Please be cautious when interpreting these results since not all aligned sequences are transcriptionally active or confer the same function in other organisms.

I hope this was helpful. If you have any more questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are publicly archived. If your question includes sensitive data, please send it instead to genom...@soe.ucsc.edu.

All the best,

Daniel Schmelter
UCSC Genome Browser

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[Daniel Schmelter]

Hello Loubna,

Thanks for clarifying your questions. I think the Genome Browser tools will be able to help you with your goals.

Since you have transcript identifiers, you can either look at them one-at-a-time or in bulk. To investigate one transcript, you can take the identifier that you are interested in and paste it into the search bar above the Browser window in the cow genome. For example, paste the identifier "NM_001034221.2" into the search bar here:

http://genome.ucsc.edu/cgi-bin/hgTracks?db=bosTau9

You should see the GATA5 transcript annotation up on bostau9's chromosome 13. You can then click View -> In Other Genomes (Convert), select hg38, and then click submit. If there is an alignment that covers most of the span, click that link to view a similar transcript in the human genome. Next, turn on Phenotype and Literature tracks of interest like ClinVar Variants, GWAS Catalog, or OMIM Alleles to investigate human variant associations. If you find something interesting in human and zoom in, you can also use the View -> In Other Genomes (Convert) tool to align back to the cow genome.

For analyzing many transcripts, you can paste your list into Table Browser's identifiers to find the transcripts' coordinates and set the output format to "BED - browser extensible data". After you click "Get Output", you will see options to show coordinates only for 3' UTR, 5' UTR, upstream, and downstream sequences. This will allow you to investigate the cow's UTRs separately if desired. Next, the LiftOver web-tool converts multiple BED coordinates to a human genome assembly and allows you to compare converted cow transcripts with human disease variants. You can do this visually with the Genome Browser by making your LiftOver output data into a Custom Track.

https://genome.ucsc.edu/cgi-bin/hgLiftOver
https://genome.ucsc.edu/cgi-bin/hgTableBrowser

To get a big picture genome similarity, you may be interested in the Cow-Human Chain alignment track.

http://genome.ucsc.edu/s/dschmelt/bosTau9HumanChain

The red regions are base coordinates that align with the human genome. You can click the track to find out where a specific region aligns. If you want to get a number for genome similarity, you use the "featureBits" utility command that gives the percent overlap between a particular dataset and the genome it is based on. This command will give you coverage, not percent identity, but it will still give some indication of genetic ancestry or distance. Here is the configuration file instructions, a link to the program download, and an example of it being run for the entire bosTau9 genome.

https://genome.ucsc.edu/goldenPath/help/mysql.html#utilities
http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64.v369/featureBits
featureBits bosTau9 chainHg38
2637967408 bases of 2715853792 (97.132%) in intersection

I hope this was helpful. 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 send it instead to genom...@soe.ucsc.edu.

All the best,

Daniel Schmelter
UCSC Genome Browser

On Fri, Jan 17, 2020 at 7:19 AM loubna el - zein <zeinl...@yahoo.com> wrote:

Dear Daniel,

Thank you for your response, I really appreciate.

I would like to know about please 

1- the percentage of genome similarity between cow and human

2- 5'UTR and 3'UTR in cow and their differences with their human ones

3- how we can explain these differences? 

thank you in advance

sincerely yours

[Daniel Schmelter]

Hello Loubna,

My name is Daniel Schmelter from the UCSC Genome Browser. You asked us a question two months ago about finding clinically relevant variants in human mapped over to the cow genome, bosTau9. We have completed this project, aligning the Human ClinVar track to a few main research organisms, including mm10, bosTau9, and danRer11. We would love to have your feedback on what you think of the new track, what suggestions you may have to make it better, and how you anticipate using such a track. We hope showing human variants in other animals is helpful to researchers and would appreciate hearing your thoughts. Here are links to a session with the clinVarLift track turned on and to the description page of the new track:

https://genome-preview.ucsc.edu/s/dschmelt/bosTau9ClinVarLift
https://genome-preview.ucsc.edu/cgi-bin/hgTrackUi?db=bosTau9&g=clinvarLift

Thank you in advance for your feedback and we hope you find this new track useful.

All the best,
Daniel Schmelter