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Use this program to retrieve the data associated with a track in text format, to calculate intersections between tracks, and to retrieve DNA sequence covered by a track. For help in using this application see Using the Table Browser for a description of the controls in this form, the User's Guide for general information and sample queries, and the OpenHelix Table Browser tutorial for a narrated presentation of the software features and usage. For more complex queries, you may want to use Galaxy or our public MySQL server. To examine the biological function of your set through annotation enrichments, send the data to GREAT. Refer to the Credits page for the list of contributors and usage restrictions associated with these data. All tables can be downloaded in their entirety from the Sequence and Annotation Downloads page.
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This section provides brief line-by-line descriptions of the Table
Browser controls. For more information on using this program, see the
Table
Browser User's Guide.
- clade: Specifies which clade the organism is in.
- genome: Specifies which organism data to use.
- assembly: Specifies which version of the organism's genome
sequence to use.
- group: Selects the type of tracks to be displayed in
the track list. The options correspond to the track groupings
shown in the Genome Browser. Select 'All Tracks' for an alphabetical list
of all available tracks in all groups. Select 'All Tables' to see all tables
including those not associated with a track.
- database: (with "All Tables" group option) Determines
which database should be used for options in table menu.
- track: Selects the annotation track data to work with. This
list displays all tracks belonging to the group specified in the
group list.
Some tracks are not available when the region is set to genome
due to the data provider's restrictions on sharing.
- table: Selects the SQL table data to use. This list shows
all tables associated with the track specified in the track
list.
Some tables may be unavailable due to the data provider's restrictions on sharing.
- describe table schema: Displays schema information for the
tables associated with the selected track.
- region: Restricts the query to a
particular chromosome or region.
Select genome to apply the query to the entire genome
(not available for certain tracks with restrictions on data sharing).
In some Human assemblies, you may select ENCODE to examine only the
ENCODE Pilot regions.
To limit the query to a specific position, type a
chromosome name, e.g. chrX, or a chromosome coordinate
range, such as chrX:100000-200000, or a gene name or other id in
the text box.
You can select multiple genomic regions by clicking the "define regions"
button and entering up to 1,000 regions in a 3- or 4-field BED file
format.
- lookup: Press this button after typing in a gene name or
other id in the position text box to look up the chromosome position
- identifiers (selected tracks only): Restricts the
output to table data that match a list of identifiers, for
instance RefSeq accessions for the RefSeq track. If no identifiers
are entered, all table data within the specified region will be
displayed.
- filter: Restricts the query to only those items that
match certain criteria, e.g. genes with a single exon. Click the
Create button to add a filter, the Edit button to
modify an existing filter, or the Clear button to remove an
existing filter.
- intersection (selected tracks only): Combines the output
of two queries into a
single set of data based on specific join criteria. For example, this
can be used to find all SNPs that intersect with RefSeq coding
regions. The intersection can be configured to retain the
existing alignment structure of the table with a specified amount of
overlap, or discard the structure in favor of a simple list of position
ranges using a base-pair intersection or union of the two data sets.
The button functionalities are similar to those of the filter
option.
- output: Specifies the output format (not all options are
available for some tracks). Formats include:
- all fields from selected table - data from the selected table
displayed in a tab-separated format suitable
for import into spreadsheets and relational databases. The ASCII
format may be read in any web browser or text editor.
- selected fields from primary and related tables - user-selected
set of tab-separated fields
from the selected table and (optionally) other related tables as well.
- sequence - DNA (or protein sequence, in some cases)
associated with the table.
- BED - positions of data items in a standard
UCSC Browser format.
- GTF - positions of all data items in a standard
gene prediction format. (Both BED and GTF formats can be
used as the basis for custom tracks).
- CDS FASTA alignment from multiple alignment
- FASTA alignments of the CDS regions of a gene prediction track
using any of the multiple alignment tracks for the current database.
Output sequence can be in either nucleotide-space or translated to
protein-space. Available only for genePred tracks.
- custom track - customized Genome Browser annotation
track based on the results of the query.
- hyperlinks to Genome Browser - returns a page full of
hyperlinks to the UCSC Genome Browser, one for each item in the table.
- data points - the data points that make up a graph
(aka wiggle) track.
- MAF - multiple alignments in MAF format
- Send output to Galaxy: displays results of query in
Galaxy, a framework for
interactive genome analysis.
- Send output to GREAT: displays the functional enrichments of the
query results in GREAT, a tool for
analysis of the biological function of cis-regulatory regions.
- file type returned: When a filename is entered in the
"output file" text box, specifies the format of the output file:
- plain text - data is in ASCII format
- gzip compressed - data is compressed in gzip format
- get output: Submits a data query based on the specified
parameters and returns the output.
- summary/statistics: Displays statistics about the data
specified by the parameters.
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