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 | + | **Select the '''Gene''' dataset, as shown [[http://www.wormbase.org 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. | ||
*Click the '''Filters''' link in the navigation panel on the left of the page; | *Click the '''Filters''' link in the navigation panel on the left of the page; | ||
| − | **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/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]], | ||
**Click '''<count>''' to see the number of genes selected, <br> | **Click '''<count>''' to see the number of genes selected, <br> | ||
| − | *Click the <span class="Apple-style-span" style="font-weight: bold;">Attributes</span> link on the navigation panel,<br> | + | *Click the <span class="Apple-style-span" style="font-weight: bold;">Attributes</span> link on the navigation panel,<br> |
| − | **Expand the '''Identification''' section; | + | **Expand the '''Identification''' section; |
| − | **Enable the '''Gene Public Name''' and''' 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"&VISIBLEPANEL=attributepanel [HERE]].<br> | + | **Enable the '''Gene Public Name''' and''' 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"&VISIBLEPANEL=attributepanel [HERE]].<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.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"&VISIBLEPANEL=resultspanel [HERE]]. | + | *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.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"&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, | ||
**Disable the''' Sequence Names (CDS) (merged)''' attribute, | **Disable the''' Sequence Names (CDS) (merged)''' attribute, | ||
| − | **Enable the <span class="Apple-style-span" style="font-weight: bold; ">Sequence Names (CDS)</span> attribute, | + | **Enable the <span class="Apple-style-span" style="font-weight: bold;">Sequence Names (CDS)</span> attribute, |
| − | **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&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"&VISIBLEPANEL=resultspanel [HERE]]. | + | **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&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"&VISIBLEPANEL=resultspanel [HERE]]. |
[[Data mining:WormMart|Index of Examples]] ... [[Data mining:WormMart:Example 2|Next->]] | [[Data mining:WormMart|Index of Examples]] ... [[Data mining:WormMart:Example 2|Next->]] | ||
Revision as of 11:16, 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 "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].
