Difference between revisions of "Data mining:WormMart:Example 1"

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*Click the&nbsp;<span class="Apple-style-span" style="font-weight: bold;">Attributes</span>&nbsp;link on the navigation panel,<br>  
 
*Click the&nbsp;<span class="Apple-style-span" style="font-weight: bold;">Attributes</span>&nbsp;link on the navigation panel,<br>  
 
**Expand the&nbsp;'''Identification'''&nbsp;section;  
 
**Expand the&nbsp;'''Identification'''&nbsp;section;  
**Enable the '''Gene Public Name''' and'''&nbsp;Sequence Names (CDS) (merged)''' attributes as shown [http://www.wormbase.org/biomart/martview?VIRTUALSCHEMANAME=default&ATTRIBUTES=wormbase_gene.default.attributes.public_name|wormbase_gene.default.attributes.gene|wormbase_gene.default.attributes.name_dmlist&FILTERS=wormbase_gene.default.filters.species_selection. "Caenorhabditis elegans"|wormbase_gene.default.filters.identity_status."Live"|wormbase_gene.default.filters.public_name."bli-1,egl-43,lag-1"&amp;VISIBLEPANEL=attributepanel [HERE]].<br>
+
**Enable the '''Gene Public Name''' and'''&nbsp;Sequence Names (CDS) (merged)''' attributes as shown [http://www.wormbase.org/biomart/martview?VIRTUALSCHEMANAME=default&ATTRIBUTES=wormbase_gene.default.attributes.public_name|wormbase_gene.default.attributes.gene|wormbase_gene.default.attributes.name_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&amp;VISIBLEPANEL=attributepanel [HERE]].<br>
  
*Click the&nbsp;'''&lt;Results&gt;'''&nbsp;button, which will load the results as shown on this&nbsp;[http://www.wormbase.org/biomart/martview?VIRTUALSCHEMANAME=default&ATTRIBUTES=wormbase_gene.default.attributes.public_name|wormbase_gene.default.attributes.gene|wormbase_gene.default.attributes.name_dmlist&FILTERS=wormbase_gene.default.filters.species_selection. "Caenorhabditis elegans"|wormbase_gene.default.filters.identity_status."Live"|wormbase_gene.default.filters.public_name."bli-1,egl-43,lag-1"&amp;VISIBLEPANEL=resultspanel [HERE]].  
+
*Click the&nbsp;'''&lt;Results&gt;'''&nbsp;button, which will load the results as shown on this&nbsp;[http://www.wormbase.org/biomart/martview?VIRTUALSCHEMANAME=default&ATTRIBUTES=wormbase_gene.default.attributes.public_name|wormbase_gene.default.attributes.gene|wormbase_gene.default.attributes.name_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&amp;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>&nbsp;page,  
 
**Return to the <span class="Apple-style-span" style="font-weight: bold;">Attributes</span>&nbsp;page,  
 
**Disable the'''&nbsp;Sequence Names (CDS) (merged)''' attribute,  
 
**Disable the'''&nbsp;Sequence Names (CDS) (merged)''' attribute,  
 
**Enable the&nbsp;<span class="Apple-style-span" style="font-weight: bold;">Sequence Names (CDS)</span>&nbsp;attribute,  
 
**Enable the&nbsp;<span class="Apple-style-span" style="font-weight: bold;">Sequence Names (CDS)</span>&nbsp;attribute,  
**Click the '''&lt;Results&gt;''' 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&FILTERS=wormbase_gene.default.filters.species_selection. "Caenorhabditis elegans"|wormbase_gene.default.filters.identity_status."Live"|wormbase_gene.default.filters.public_name."bli-1,egl-43,lag-1"&amp;VISIBLEPANEL=resultspanel [HERE]].
+
**Click the '''&lt;Results&gt;''' 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&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&amp;VISIBLEPANEL=resultspanel [HERE]].
  
 
[[Data mining:WormMart|Index of Examples]] ... [[Data mining:WormMart:Example 2|Next-&gt;]]
 
[[Data mining:WormMart|Index of Examples]] ... [[Data mining:WormMart:Example 2|Next-&gt;]]

Revision as of 11:35, 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 [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 [HERE].
  • 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].

Index of Examples ... Next->