[Genome] Link between and the gene ontology database

[Rachel Harte]

Marcel,

There is no direct link between these tables. However, you can intersect
regions of the genome using the Table Browser. For instance, if you would
like to find the regions that are upstream of knownGene that contain
repeats, you can do in two steps. First, you will need to create a custom
track of the upstream regions and then you can intersect it with the
repeats track.

Here is information about the Table Browser:
http://genome.ucsc.edu/cgi-bin/hgTables?command=start#Help

To start using it, click on the Tables link on the top blue menu bar.
Then follow these steps to create a custom track of upstream regions:
1) Select Genome: Human Assembly: May 2004
May 2004 is hg17
2) Select "Genes and Gene Prediction Tracks" at the group and "Known
Genes" as the track and knownGene as the table.
3) Select "custom track" as the output format and press "get output"
4) Select "Create one BED record per:"
Upstream by    bases
and fill in the number of bases upstream of Known Genes.
5) Press "get custom track in table browser"

Now you can intersect it with the repeats track:
1) select "Custom Tracks" as the group and then you can select the track
that you made.
2) Press the "create" button for intersection
3) Select "Variation and Repeats" as the group and "RepeatMasker" as the
track.
4) Then once you have submitted this, select BED as the output format and
get the output. This will give you a list known genes upstream regions
that contain repeats.

This is just an example of what you can do. You can probably do something
similar to look for genes close to some DNA elements.

You can also find tables for the go database in the Table Browser. If you
select "All Tables" for the group, then "go" will appear in the database
list. You can select a go table in the table list and then press "describe
table schema" to get the description of the table and also other tables
that are linked to it. So that may help with figuring out which tables may
be linked when making mySQL queries.

I hope that this helps you. Please let us know if you need further
assistance.

Rachel

Marcel Leonce GUIBOTSY M'BOULAS guibot04 at hotmail.com
Fri Dec 29 13:42:56 PST 2006


Dear all,

I downoloaded the knowngene of hg17, the repeatmasker and the gene
ontology
mysql-tables. I want to get the name of genes close to some DNA elements.
Mysql queries always return an empty set. There seems to be no link
between
these tables. What should I do to solve this issue? I'm new in MySQL.

Happy holidays

Thank you.

Marcel Leonce Guibotsy
mguibotsy at uta.edu
Research Assistant
University of Texas at Arlington


Rachel Harte
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu