Difference between revisions of "Data mining:WormMart:Example 1"
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*On initial page; | *On initial page; | ||
**Select the latest database release, | **Select the latest database release, | ||
| − | **Select the '''Gene''' dataset, as shown [http://www.wormbase.org/biomart/martview?VIRTUALSCHEMANAME=default&ATTRIBUTES=wormbase_gene.default.attributes.gene|wormbase_gene.default.attributes.public_name&FILTERS=wormbase_gene.default.filters.species_selection. "Caenorhabditis elegans"|wormbase_gene.default.filters.identity_status."Live"&VISIBLEPANEL=mainpanel HERE]]. | + | **Select the '''Gene''' dataset, as shown [http://www.wormbase.org/biomart/martview?VIRTUALSCHEMANAME=default&ATTRIBUTES=wormbase_gene.default.attributes.gene|wormbase_gene.default.attributes.public_name&FILTERS=wormbase_gene.default.filters.species_selection. "Caenorhabditis elegans"|wormbase_gene.default.filters.identity_status."Live"&VISIBLEPANEL=mainpanel [HERE]]. |
**The '''<count>''' button on the top left of the page will report the number of genes in the dataset. | **The '''<count>''' button on the top left of the page will report the number of genes in the dataset. | ||
Revision as of 11:21, 21 May 2008
Example 1: List all synonyms for the following genes; bli-1, egl-43, lag-1
- Start a new WormMart query: [HERE].
- On initial page;
- Select the latest database release,
- Select the Gene dataset, as shown "Caenorhabditis elegans"|wormbase_gene.default.filters.identity_status."Live"&VISIBLEPANEL=mainpanel [HERE].
- The <count> button on the top left of the page will report the number of genes in the dataset.
- Click the Filters link in the navigation panel on the left of the page;
- Expand the Identification section by clicking on it,
- Enable the Limit to Gene ID(s) of Type - Public/CGC Name filter,
- Paste the gene IDs bli-1, egl-43, lag-1 into the text box, as shown [HERE],
- Click <count> to see the number of genes selected,
- Click the Attributes link on the navigation panel,
- Expand the Identification section;
- Enable the Gene Public Name and Sequence Names (CDS) (merged) attributes as shown "Caenorhabditis elegans"|wormbase_gene.default.filters.identity_status."Live"|wormbase_gene.default.filters.public_name."bli-1,egl-43,lag-1"&VISIBLEPANEL=attributepanel [HERE].
- Click the <Results> button, which will load the results as shown on this "Caenorhabditis elegans"|wormbase_gene.default.filters.identity_status."Live"|wormbase_gene.default.filters.public_name."bli-1,egl-43,lag-1"&VISIBLEPANEL=resultspanel [HERE].
- Note that the gene synonyms in the export are combined in a single table cell. To get a row per synonym rather than a row per gene;
- Return to the Attributes page,
- Disable the Sequence Names (CDS) (merged) attribute,
- Enable the Sequence Names (CDS) attribute,
- Click the <Results> button, which will load the results as shown on this "Caenorhabditis elegans"|wormbase_gene.default.filters.identity_status."Live"|wormbase_gene.default.filters.public_name."bli-1,egl-43,lag-1"&VISIBLEPANEL=resultspanel [HERE].
