Cross-Database Gene Annotation: Mapping Ensembl and UCSC Gene IDs

Ensembl and UCSC are two popular genome databases, each using its own unique gene identifiers. To annotate Ensembl genes using UCSC gene IDs, you'll need to map the Ensembl gene IDs to their corresponding UCSC gene IDs.

You can use the BioMart tool provided by Ensembl to perform this conversion. Here's a step-by-step guide on how to do this:

1. Go to the Ensembl BioMart website: http://www.ensembl.org/biomart/martview

2. Select the appropriate Ensembl database under "CHOOSE DATABASE" (e.g., Ensembl Genes for the genes database).

3. Under "CHOOSE DATASET," select the appropriate species (e.g., Homo sapiens genes for human genes).

4. In the "Filters" tab, you can apply any specific filters to your search if necessary (e.g., if you want to limit your search to a particular chromosome or gene biotype).

5. In the "Attributes" tab, select the desired gene attributes for your output. You'll want to include at least the following attributes:

   • Ensembl Gene ID
   • Associated Gene Name
   • UCSC Gene ID

6. Click "Results" in the top left corner to generate the output table. You can export the table in different formats, such as CSV or TSV.

Now you have a table that maps Ensembl gene IDs to their corresponding UCSC gene IDs and associated gene names. You can use this table to annotate your Ensembl genes using UCSC gene IDs in your analysis.

To map UCSC gene IDs to Ensembl gene IDs, you can use the BioMart tool provided by Ensembl. Here's a step-by-step guide on how to perform this conversion:

1. Go to the Ensembl BioMart website: http://www.ensembl.org/biomart/martview

2. Select the appropriate Ensembl database under "CHOOSE DATABASE" (e.g., Ensembl Genes for the genes database).

3. Under "CHOOSE DATASET," select the appropriate species (e.g., Homo sapiens genes for human genes).

4. In the "Filters" tab, click on the "EXTERNAL REFERENCE ID LIST LIMITS" section to expand it. Then, select "UCSC Gene ID(s)" from the dropdown list and paste your list of UCSC gene IDs into the text box.

5. In the "Attributes" tab, select the desired gene attributes for your output. You'll want to include at least the following attributes:

   • Ensembl Gene ID
   • Associated Gene Name
   • UCSC Gene ID

6. Click "Results" in the top left corner to generate the output table. You can export the table in different formats, such as CSV or TSV.

Now you have a table that maps UCSC gene IDs to their corresponding Ensembl gene IDs and associated gene names. You can use this table to annotate your UCSC genes using Ensembl gene IDs in your analysis.

An alternative method for converting UCSC gene IDs to Ensembl gene IDs is utilizing the UCSC Table Browser, which offers a convenient way to perform this conversion. Follow these steps to perform the conversion:

1. Go to the UCSC Table Browser: https://genome.ucsc.edu/cgi-bin/hgTables

2. Choose the appropriate settings for your search:

   • "clade": Mammal (or the appropriate clade for your species)
   • "genome": Human (or the appropriate genome for your species)
   • "assembly": GRCh38/hg38 (or the appropriate assembly version for your species)

3. Select the "knownGene" table in the "group" dropdown menu, and "knownGene" in the "track" dropdown menu.

4. Change the "output format" to "selected fields from primary and related tables."

5. Click the "get output" button.

6. In the "Select Fields from hg38.knownGene" section, check the boxes for "name" (UCSC gene ID) and "chrom" (chromosome). In the "Linked Tables" section, check the box for "ensemblToGeneName" (Ensembl gene ID). You can also select additional fields as needed.

7. Click the "get output" button.

8. The resulting table will contain the UCSC gene IDs, chromosome information, and the corresponding Ensembl gene IDs. You can use this table to map UCSC gene IDs to Ensembl gene IDs in your analysis.

Note that this method is based on the UCSC Table Browser's available data, which may not be as up-to-date as the data available in Ensembl BioMart. However, it can still be a useful alternative tool for gene ID conversion.

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