How to download tissue-specific hg19 ESTs

[Weisheng Wu]

Hi,

I'm able to visualize tissue-specific ESTs using the Human EST track. It allows me to color a specific tissue. But I can't figure out how to download the tissue-specific data. I downloaded the human EST track table data, but there is no tissue information there.

For example, I could search for an EST "DA829895" and click it in the browser. This gives me a page with the detailed information of it. It has tissue information: "Clone: PLACE1004029". If I, for example, want to download all ESTs from placenta tissue, how should I do that?

Thanks.

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Weisheng Wu, Ph.D.

Research Area Specialist Sr.
BRCF Bioinformatics Core
022-1012 NCRC

University of Michigan, Ann Arbor, 48109

wei...@umich.edu
734-647-3022

[Luvina Guruvadoo]

Hello Weisheng,

Thanks for your question. The tissue information is actually contained within a different table. You could use the Table Browser and create a filter to search for ESTs found in placenta tissue, however, this is quite a large query and may cause the Browser to timeout. I suggest connecting to our public MySQL server and creating your own query. You can read more on how to use our public MySQL server here: http://genome.ucsc.edu/FAQ/FAQdownloads#download29. The related tables are "gbCdnaInfo" and "tissue". You can use the describe schema button on the Table Browser to help you understand and join the correct tables/fields. Also see this archived question: https://groups.google.com/a/soe.ucsc.edu/d/msg/genome/CvkSufQczCk/DHZiE7BW5YAJ

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 forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

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Luvina Guruvadoo
UCSC Genome Bioinformatics Group

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[Weisheng Wu]

Hi Luvina,

Thanks a lot for your explanation. It's quite helpful!

Yes I realized that I had to use both "gbDdnaInfo" and "tissue" tables. My problem now is that I can't find the "tissue" table. It's not under human ESTs track.

Could you direct me to the location of that table? Thanks.

Weisheng

[Steve Heitner]

Hello, Weisheng.

The tissue table is linked to the all_est table through the gbCdnaInfo table.  You can also obtain this information through our Table Browser.  If you are unfamiliar with the Table Browser, please also see the User’s Guide at http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html.

Also note that the tissue table contains many entries related to placenta.  To get all entries, we will be using a wildcard in our filter.  Once you see all of the entries, you may choose to refine your filter based on the items showing up in your results.  To obtain the information you are interested in, perform the following steps:

1. Navigate to http://genome.ucsc.edu/cgi-bin/hgTables

2. Select the following options:
Clade: Mammal
Genome: Human
Assembly: Feb. 2009 (GRCh37/hg19)
Group: mRNA and EST
Track: Human ESTs
Region: select “genome” for the entire genome; select “position” to specify a single genomic locus; click the “define regions” button to specify multiple genomic loci
Output format: selected fields from primary and related tables

3. On the “filter” line, click the “create” button

4. In the “Linked Tables” section, check the “hg19.gbCdnaInfo” checkbox

5. At the bottom of the page, click the “allow filtering using fields in checked tables” button

6. In the “Linked Tables” section, check the “hg19.tissue” checkbox

7. Click the “allow filtering using fields in checked tables” button

8. In the “hg19.tissue based filters” section, the “Free-form query” box should read EXACTLY: name like “%placenta%”

9. Click the “submit” button

10. Click the “get output” button

11. You can add fields from the “gbCdnaInfo” and “tissue” tables the same way you did for the filter in steps 4-7

12. Check the checkboxes of the fields you would like to see in your output

13. Click the “get output” button

Please contact us again at gen...@soe.ucsc.edu if you have any further questions.  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.

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Steve Heitner
UCSC Genome Bioinformatics Group

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