|
|
(11 intermediate revisions by 2 users not shown) |
Line 1: |
Line 1: |
− | === Example 1: List all synonyms for the following genes; bli-1, egl-43, lag-1 === | + | === 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]]. | + | *Start a new WormMart query: [http://caprica.caltech.edu:9002/biomart/martview/ [HERE]]. |
| | | |
− | * On the '''START''' page; | + | *On initial page; |
− | ** Select the '''Gene''' dataset. | + | **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]]. | + | **Select the '''Gene''' dataset, |
− | ** Click '''<next>''' to proceed to the '''FILTER''' page.
| + | **The '''<count>''' button on the top left of the page will report the number of genes in the dataset. |
| | | |
− | * On the '''FILTER''' page; | + | *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, | + | **Expand the '''Identification''' section by clicking on it, |
− | ** Paste the gene IDs '''bli-1, egl-43, lag-1''' into the text box, | + | **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]] | + | **Paste the gene IDs '''bli-1, egl-43, lag-1''' into the text box, |
− | ** Click '''<next>''' to proceed to the OUTPUT page.
| + | **Click '''<count>''' to see the number of genes selected, <br> |
| | | |
− | * On the '''OUTPUT''' page, in the '''IDENTIFICATION - IDs''' section; | + | *Click the <span class="Apple-style-span" style="font-weight: bold;">Attributes</span> 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]] | + | **Expand the '''Identification''' section; |
− | ** Click the '''<export>''' 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]].
| + | **Enable the '''Gene Public Name''' and''' 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; | + | *Click the '''<Results>''' 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_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, | + | *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, | + | **Return to the <span class="Apple-style-span" style="font-weight: bold;">Attributes</span> page, |
− | ** Enable the ''' Gene Name (All)''' attribute, | + | **Disable the''' Sequence Names (CDS) (merged)''' attribute, |
− | ** Click the '''<export>''' 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]]. | + | **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://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->]] | + | [[Data mining:WormMart|Index of Examples]] ... [[Data mining:WormMart:Example 2|Next->]] |
| + | |
| + | |
| + | [[Category:User Guide]] |