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,  
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**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%20elegans"|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.%22Caenorhabditis%20elegans%22|wormbase_gene.default.filters.identity_status.%22Live%22&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.
  
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**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, as shown [http://www.wormbase.org/biomart/martview/martview?gene_species_selection=Brugia%20pahangi&gene_species_selection_last=Brugia%20pahangi&gene_collection_id_list_toggle=1&gene_id_list_options=public_name&gene_id_list_options_list=bli-1%2Cegl-43%2Clag-1&gene_gene_class=aak&gene_gene_class_last=aak&gene_chromosome_name=I&gene_chromosome_name_last=I&gene_chromosome_strand=-1&gene_chromosome_strand_last=-1&gene_has_annotation_options_filter=has_concise_description&gene_has_annotation_options=Only&gene_identity_status=Dead&gene_identity_status_last=Dead&gene_history_action=Acquires_merge&gene_history_action_last=Acquires_merge&gene_prediction_status=Confirmed&gene_prediction_status_last=Confirmed&gene_coding_status=coding&gene_coding_status_last=coding&gene_utr_status=utr5%2Butr3&gene_utr_status_last=utr5%2Butr3&gene_ortholog_gene=Caenorhabditis%20briggsae&gene_ortholog_gene_last=Caenorhabditis%20briggsae&gene_rnai_phenotype_options=Aberrant%20Cytoplasmic%20Structures&gene_rnai_phenotype_options_last=Aberrant%20Cytoplasmic%20Structures&default_link=---&default_link_last=---&stage=filter&schema=WS_CURRENT&collection_seq_scope_type=transcript_exon_intron&dataset_last=gene&stage_initialised=start&stage_initialised=filter&outformat=html&stage_prev=filter&seq_scope=tscr&gene_has_annotation_options_last=Only&outcompress=none&dataset=gene&status_count_start=44663&gene_id_list_options_last=public_name&gene_annotation_list_options_last=operon&status_count_filter=3 [HERE]],  
+
**Paste the gene IDs '''bli-1, egl-43, lag-1''' into the text box, 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.%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=filterpanel [HERE]],  
 
**Click '''&lt;count&gt;''' to see the number of genes selected,&nbsp;<br>
 
**Click '''&lt;count&gt;''' to see the number of genes selected,&nbsp;<br>
  

Revision as of 11:31, 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, 

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