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

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=== Example 1: List all synonyms for the following genes; bli-1, egl-43, lag-1 ===
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=== Example 1: List all synonyms for the following genes; bli-1, egl-43, lag-1 ===
  
* Start a new WormMart query: [http://www.wormbase.org/biomart/martview [HERE]].
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*Start a new WormMart query: [http://caprica.caltech.edu:9002/biomart/martview/ [HERE]].
  
* On the '''START''' page;
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*On initial page;  
** Select the '''Gene''' dataset.
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**Select the latest database release,
** The '''<count>''' button on the right of the page will report the number of genes in the dataset in the '''Summary''' section, as shown [http://www.wormbase.org/biomart/martview/martview?schema=WS_CURRENT&dataset=gene&stage=start&stage_prev=start&stage_initialised=start [HERE]].
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**Select the '''Gene''' dataset, 
** Click '''<next>''' to proceed to the '''FILTER''' page.
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**The '''<count>''' button on the top left of the page will report the number of genes in the dataset.
  
* On the '''FILTER''' page;
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*Click the '''Filters''' link in the navigation panel on the left of the page;  
** In the '''Identification''' section, enable the '''Limit to Gene ID(s) of Type - Public/CGC Name''' filter,
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**Expand the '''Identification''' section by clicking on it,  
** Paste the gene IDs '''bli-1, egl-43, lag-1''' into the text box,
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**Enable the '''Limit to Gene ID(s) of Type - Public/CGC Name''' filter,  
** Click '''<count>''' to update the page, 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]]
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**Paste the gene IDs '''bli-1, egl-43, lag-1''' into the text box,  
** Click '''<next>''' to proceed to the OUTPUT page.
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**Click '''&lt;count&gt;''' to see the number of genes selected,&nbsp;<br>
  
* On the '''OUTPUT''' page, in the '''IDENTIFICATION - IDs''' section;
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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>
** Enable the '''Gene Public Name''' and '''Gene Names (merged)''' attributes as shown [http://www.wormbase.org/biomart/martview/martview?outtype=feature&collection_gene_id=gene&collection_gene_id=public_name&collection_gene_id=name_dmlist&outformat=html&outcompress=none&stage=output&collection_seq_scope_type_this=dna.transcript_exon_intron&schema=WS_CURRENT&default_link=---&gene_history_action=Acquires_merge&gene_gene_class=aak&gene_has_annotation_options=Only&dataset_last=gene&collection_molecular=seq_cds_name&seq_scope=tscr&gene_chromosome_name=I&status_count_filter=3&gene_ortholog_gene_last=Caenorhabditis%20briggsae&gene_utr_status_last=utr5%2Butr3&gene_ortholog_gene=Caenorhabditis%20briggsae&collection_gene=seq_wb_gene_id&collection_gene=seq_public_name&gene_id_list_options_last=public_name&gene_collection_id_list_toggle=1&gene_id_list_options_list=bli-1%2Cegl-43%2Clag-1&gene_species_selection=Brugia%20pahangi&default_link_last=---&gene_prediction_status=Confirmed&gene_history_action_last=Acquires_merge&collection_seq_scope_type=transcript_exon_intron&gene_id_list_options=public_name&gene_coding_status_last=coding&gene_chromosome_strand=-1&stage_initialised=start&stage_initialised=filter&stage_initialised=output&gene_utr_status=utr5%2Butr3&stage_prev=output&gene_chromosome_strand_last=-1&gene_prediction_status_last=Confirmed&gene_identity_status=Dead&gene_coding_status=coding&gene_has_annotation_options_last=Only&gene_species_selection_last=Brugia%20pahangi&gene_chromosome_name_last=I&gene_rnai_phenotype_options=Aberrant%20Cytoplasmic%20Structures&gene_has_annotation_options_filter=has_concise_description&collection_structure=exon_name&gene_rnai_phenotype_options_last=Aberrant%20Cytoplasmic%20Structures&gene_identity_status_last=Dead&dataset=gene&gene_gene_class_last=aak&status_count_start=44663&status_count_output=3 [HERE]]
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**Expand the&nbsp;'''Identification'''&nbsp;section;  
** Click the '''&lt;export&gt;''' button, which will load the results as shown on this [http://www.wormbase.org/biomart/martview/martview?outtype=feature&collection_gene_id=gene&collection_gene_id=public_name&collection_gene_id=name_dmlist&outformat=html&outcompress=none&stage=output&collection_seq_scope_type_this=dna.transcript_exon_intron&schema=WS_CURRENT&default_link=---&gene_history_action=Acquires_merge&gene_gene_class=aak&gene_has_annotation_options=Only&dataset_last=gene&collection_molecular=seq_cds_name&seq_scope=tscr&gene_chromosome_name=I&status_count_filter=3&gene_ortholog_gene_last=Caenorhabditis%20briggsae&gene_utr_status_last=utr5%2Butr3&gene_ortholog_gene=Caenorhabditis%20briggsae&collection_gene=seq_wb_gene_id&collection_gene=seq_public_name&gene_id_list_options_last=public_name&gene_collection_id_list_toggle=1&gene_id_list_options_list=bli-1%2Cegl-43%2Clag-1&gene_species_selection=Brugia%20pahangi&default_link_last=---&gene_prediction_status=Confirmed&gene_history_action_last=Acquires_merge&collection_seq_scope_type=transcript_exon_intron&gene_id_list_options=public_name&gene_coding_status_last=coding&gene_chromosome_strand=-1&stage_initialised=start&stage_initialised=filter&stage_initialised=output&gene_utr_status=utr5%2Butr3&stage_prev=output&gene_chromosome_strand_last=-1&gene_prediction_status_last=Confirmed&gene_identity_status=Dead&gene_coding_status=coding&gene_has_annotation_options_last=Only&gene_species_selection_last=Brugia%20pahangi&gene_chromosome_name_last=I&gene_rnai_phenotype_options=Aberrant%20Cytoplasmic%20Structures&gene_has_annotation_options_filter=has_concise_description&collection_structure=exon_name&gene_rnai_phenotype_options_last=Aberrant%20Cytoplasmic%20Structures&gene_identity_status_last=Dead&dataset=gene&gene_gene_class_last=aak&status_count_start=44663&status_count_output=3&_export=1 [HERE]].
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**Enable the '''Gene Public Name''' and'''&nbsp;Sequence Names (CDS) (merged)''' attributes.<br>
  
* 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;
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*Click the&nbsp;'''&lt;Results&gt;'''&nbsp;button, which will load the results as shown on this&nbsp;[http://caprica.caltech.edu:9002/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]].
** Return to the '''OUTPUT''' page,
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*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;  
** Disable the '''Gene Names (merged)''' attribute,
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**Return to the <span class="Apple-style-span" style="font-weight: bold;">Attributes</span>&nbsp;page,  
** Enable the ''' Gene Name (All)''' attribute,
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**Disable the'''&nbsp;Sequence Names (CDS) (merged)''' attribute,  
** Click the '''&lt;export&gt;''' button, which will load the results as shown on this [http://www.wormbase.org/biomart/martview/martview?outtype=feature&collection_gene_id=gene&collection_gene_id=public_name&collection_gene_id=name&outformat=html&outcompress=none&stage=output&collection_seq_scope_type_this=dna.transcript_exon_intron&schema=WS_CURRENT&default_link=---&gene_history_action=Acquires_merge&gene_gene_class=aak&gene_has_annotation_options=Only&dataset_last=gene&collection_molecular=seq_cds_name&seq_scope=tscr&gene_chromosome_name=I&status_count_filter=3&gene_ortholog_gene_last=Caenorhabditis%20briggsae&gene_utr_status_last=utr5%2Butr3&gene_ortholog_gene=Caenorhabditis%20briggsae&collection_gene=seq_wb_gene_id&collection_gene=seq_public_name&gene_id_list_options_last=public_name&gene_collection_id_list_toggle=1&gene_id_list_options_list=bli-1%2Cegl-43%2Clag-1&gene_species_selection=Brugia%20pahangi&default_link_last=---&gene_prediction_status=Confirmed&gene_history_action_last=Acquires_merge&collection_seq_scope_type=transcript_exon_intron&gene_id_list_options=public_name&gene_coding_status_last=coding&gene_chromosome_strand=-1&stage_initialised=start&stage_initialised=filter&stage_initialised=output&gene_utr_status=utr5%2Butr3&stage_prev=output&gene_chromosome_strand_last=-1&gene_prediction_status_last=Confirmed&gene_coding_status=coding&gene_identity_status=Dead&gene_has_annotation_options_last=Only&gene_chromosome_name_last=I&gene_species_selection_last=Brugia%20pahangi&gene_rnai_phenotype_options=Aberrant%20Cytoplasmic%20Structures&gene_has_annotation_options_filter=has_concise_description&collection_structure=exon_name&gene_rnai_phenotype_options_last=Aberrant%20Cytoplasmic%20Structures&gene_identity_status_last=Dead&dataset=gene&gene_gene_class_last=aak&status_count_start=44663&status_count_output=3&_export=1 [HERE]].
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**Enable the&nbsp;<span class="Apple-style-span" style="font-weight: bold;">Sequence Names (CDS)</span>&nbsp;attribute,  
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**Click the '''&lt;Results&gt;''' button, which will load the results as shown on this [http://caprica.caltech.edu:9002/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&VISIBLEPANEL=resultspanel [HERE]].
  
[[Data_mining:WormMart|Index of Examples]] ... [[Data_mining:WormMart:Example_2|Next-&gt;]]
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[[Data mining:WormMart|Index of Examples]] ... [[Data mining:WormMart:Example 2|Next-&gt;]]
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[[Category:User Guide]]

Latest revision as of 10:41, 31 January 2013

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].

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