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The UCSC Genome Browser

Table Browser

The UCSC Genome Browser is built on a series of SQL tables.  However, the details in all of these tables cannot be fully viewed in the graphical browser view.  For that reason, UCSC gives users a way to search or browse the tables to extract data that cannot be gathered from the browser view.

To get to tables directly related to your area of interest, from the Genome Browser window, go to the top menu bar, select Tools -> Table Browser.  To access the table browser without starting from a genomic region, the Table Browser is available in the top menu bar in the same place: Tools -> Table Browser. The difference between accessing the Table Browser from within the Genome Browser or from the home page is that, from within the Genome Browser, the link to the Table Browser will pre-load your region of interest.

Screen shot of table browser.

 

The Table Browser set-up page has many options:

  • Set your species of choice and assembly

  • Choose your targets from the group menu: default is Genes & Gene Predictions, but you can access table data on variation, regulation, disease annotation and much more

  • Use the region you have been viewing (indicated by the position radio button and text box) or chose the entire genome (not recommended, due to massive amounts of data from whole genome tables)  

    • Use the lookup button to look up an area by a gene name

    • Use the define regions button to paste or upload a file of genomic coordinates

  • Paste or upload a list of identifiers (works only for specific tracks, like RefSeq accession numbers for RefSeq gene tracks)

  • Filter by inputting specific gene symbols to search under, or by entering specific sequence for short repeats, or by many other filter options.  The filter create button will open a new window where you can set your filter preferences

  • Create an intersection between two tables within the genome browser's database

  • Output files as simple text, hyperlinks, BED files, FASTA aligments, for Galaxy analysis suite and more

  • Use the summary/statistics button to get a preview of how much data will be returned in your tables before you actually request the output

The Table Browser can be particularly useful for finding transcription start and end sites, which are not always the same as the CDS regions, plus exact coordinates for each exon start and end site for a particular gene.  These features are not available in the browser view.