Hello Sufen, The Table browser can retrieve information in batch based on identifiers. It can also be used to link between tracks (when a common key exists) and to perform overlap comparisons.
Your example is slightly complicated, because the identifier is an Ensembl gene, not an Ensembl transcript. I list the methods for using both and how to move between the two. Main methods: 1) If you have or could get transcript identifiers, then you can select the Ensembl Gene track in the Table browser, paste or upload the set of identifiers, and extract alignment information from that track. At the output stage, you could also link in other data by using the output format "all fields from selected and related tables". The knownToEnsembl table would allow access to the UCSC Gene's track annotation. Or, you could perform an intersection against another positional data track (example, the MGI tracks in group Phenotype and Allele). 2) If you only have gene identifiers, then download the entire primary table for the track (using the Table browser or ftp to Downloads), compare your list of gene identifiers versus the column "name2", and extract annotation lines. Data can be loaded back as a custom track, you can compare to other tracks using the intersection function (coordinate overlap). If you want to compare based on common data keys, you will need to download the tables as text files and create your own tools, as custom tracks do not have the required common keys stored in the database to allow output type "all fields from selected and related tables". You may want to start with #2, then go to #1. In #2, only extract transcript identifiers (column "name") instead of the entire data row, then use those identifiers as input for #1. Other methods: 3) Use the Table browser to understand the schema, ftp all data files from the Downloads server, and create your own command line tools to link/parse the data. 4) Use the Table browser to understand the schema, then use direct mySQL access to create your own queries to link the data and save output. Use command line tools to parse as needed. Table browser help: http://genome-test.cse.ucsc.edu/goldenPath/help/hgTablesHelp.html Download help: http://genome-test.cse.ucsc.edu/FAQ/FAQdownloads.html#download1 Direct mySQL help: http://genome-test.cse.ucsc.edu/FAQ/FAQdownloads.html#download29 Hopefully one of these options will work for you. Please let us know if you have questions, Jennifer --------------------------------- Jennifer Jackson UCSC Genome Informatics Group http://genome.ucsc.edu/ On 3/24/10 11:50 AM, Sufen Hu wrote: > Hello, > > Is there any way in UCSC that I input a list of gene ID and get all gene > annotation. For example, I input gene ID ENSMUSG00000053277 > , then I get information such as EG623015 (MGI (automatic)) > > Thanks a lot. > > Sufen > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
