Difference between revisions of "Data mining:WormMart:Example 1"
From WormBaseWiki
Jump to navigationJump to search| Line 5: | Line 5: | ||
*On initial page; | *On initial page; | ||
**Select the latest database release, | **Select the latest database release, | ||
| − | **Select the '''Gene''' dataset, | + | **Select the '''Gene''' dataset, |
**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. | ||
| Line 11: | Line 11: | ||
**Expand the '''Identification''' section by clicking on it, | **Expand the '''Identification''' section by clicking on it, | ||
**Enable the '''Limit to Gene ID(s) of Type - Public/CGC Name''' filter, | **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, | + | **Paste the gene IDs '''bli-1, egl-43, lag-1''' into the text box, |
**Click '''<count>''' to see the number of genes selected, <br> | **Click '''<count>''' to see the number of genes selected, <br> | ||
| Line 18: | Line 18: | ||
**Enable the '''Gene Public Name''' and''' Sequence Names (CDS) (merged)''' attributes.<br> | **Enable the '''Gene Public Name''' and''' Sequence Names (CDS) (merged)''' attributes.<br> | ||
| − | *Click the '''<Results>''' button, which will load the results as shown on this [http://www.wormbase.org/biomart/martview?VIRTUALSCHEMANAME=default&ATTRIBUTES=wormbase_gene.default.attributes.public_name|wormbase_gene.default.attributes.gene|wormbase_gene.default.attributes. | + | *Click the '''<Results>''' button, which will load the results as shown on this [http://www.wormbase.org/biomart/martview?VIRTUALSCHEMANAME=default&ATTRIBUTES=wormbase_gene.default.attributes.public_name|wormbase_gene.default.attributes.gene|wormbase_gene.default.attributes.cds_dmlist&FILTERS=wormbase_gene.default.filters.species_selection.%22Caenorhabditis%20elegans%22|wormbase_gene.default.filters.identity_status.%22Live%22|wormbase_gene.default.filters.public_name.%22bli-1,egl-43,lag-1%22&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; | *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 <span class="Apple-style-span" style="font-weight: bold;">Attributes</span> page, | **Return to the <span class="Apple-style-span" style="font-weight: bold;">Attributes</span> page, | ||
Revision as of 11:40, 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,
- 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,
- 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.
- Click the <Results> button, which will load the results as shown on this [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 [HERE].
