Difference between revisions of "Data mining:WormMart:Example 3"

From WormBaseWiki
Jump to navigationJump to search
Line 5: Line 5:
  
 
*Within the <span class="Apple-style-span" style="font-weight: bold;">Filter</span>&nbsp;section;  
 
*Within the <span class="Apple-style-span" style="font-weight: bold;">Filter</span>&nbsp;section;  
−
**Under&nbsp;'''Phenotype''', Enable the&nbsp;<span class="Apple-style-span" style="font-size: 16px; line-height: normal; -webkit-border-horizontal-spacing: 2px; -webkit-border-vertical-spacing: 2px; "><span class="Apple-style-span" style="font-weight: bold;">Limit to Phenotype Primary Name</span></span>&nbsp;filter, and select the '''embryonic lethal''' option,  
+
**Under&nbsp;'''Phenotype''', Enable the&nbsp;<span class="Apple-style-span" style="font-size: 16px; line-height: normal; -webkit-border-horizontal-spacing: 2px; -webkit-border-vertical-spacing: 2px;"><span class="Apple-style-span" style="font-weight: bold;">Limit to Phenotype Primary Name</span></span>&nbsp;filter, and select the '''embryonic lethal''' option,  
 
*Within the lower&nbsp;'''Dataset''' section;  
 
*Within the lower&nbsp;'''Dataset''' section;  
−
**For the '''Second Dataset''' select '''GO Term''' as we will use this dataset to filter for serine/threonone kinases,
+
**For the '''Second Dataset''' select '''GO Term''' as we will use this dataset to filter for serine/threonone kinases,  
−
**Within the Go Term's <span class="Apple-style-span" style="font-weight: bold;">Filter</span>&nbsp;section,&nbsp;Enable the&nbsp;'''Limit to GO Term ID(s)'''&nbsp;filter, and enter&nbsp;<span class="Apple-style-span" style="font-weight: bold; ">GO:0004674 (<span class="Apple-style-span" style="font-weight: normal; ">protein serine/threonine kinase activity)</span>.&nbsp;</span><span class="Apple-style-span" style="font-weight: bold;">
+
**Within the Go Term's <span class="Apple-style-span" style="font-weight: bold;">Filter</span>&nbsp;section,&nbsp;Enable the&nbsp;'''Limit to GO Term ID(s)'''&nbsp;filter, and enter&nbsp;<span class="Apple-style-span" style="font-weight: bold;">GO:0004674 (<span class="Apple-style-span" style="font-weight: normal;">protein serine/threonine kinase activity)</span>.&nbsp;</span><span class="Apple-style-span" style="font-weight: bold;">
 
</span>
 
</span>
 +
 +
  
 
*Within the RNAi <span class="Apple-style-span" style="font-weight: bold;">Attribute</span>&nbsp;section;  
 
*Within the RNAi <span class="Apple-style-span" style="font-weight: bold;">Attribute</span>&nbsp;section;  
Line 15: Line 17:
 
**In the '''Phenotype''' section, select '''Observed Phen Info (merged)''',  
 
**In the '''Phenotype''' section, select '''Observed Phen Info (merged)''',  
 
**In the '''Inhibits Gene''' section, select '''Gene Info (merged)''',  
 
**In the '''Inhibits Gene''' section, select '''Gene Info (merged)''',  
−
**In the '''Experiment''' section, select '''Author (merged)'''  
+
**In the '''Experiment''' section, select '''Author (merged)'''
−
**The above selection is shown [http://www.wormbase.org/biomart/martview/martview?collection_rnai=rnai&collection_phenotype_summary=phenotype_observed_dminfo&collection_inhibits=inhibits_gene_dminfo&collection_experiment=author_dmlist&outformat=html&outcompress=none&stage=output&wormbase_rnai_phenotype_select=embryonic_lethal&wormbase_rnai_laboratory_last=aa&wormbase_gene_species_selection=caenorhabditis_elegans&schema=WS_CURRENT&default_link=wormbase_gene_id&outtype=feature_page&dataset_last=wormbase_rnai&wormbase_rnai_has_experiment_options_filter=experiment_author_count&wormbase_go_term_goterm_id_list_options_last=go_term&second_dataset=wormbase_go_term&wormbase_go_term_collection_goterm_id_list_toggle=1&wormbase_rnai_has_annotation_options=Only&wormbase_gene_homolog_blastp_evalue=100&seq_scope=tscr&status_count_filter=-1&wormbase_rnai_has_phenotype_annotation_options_last=Only&wormbase_rnai_phenotype_status_options=Only&wormbase_gene_rnai_phenotype_status_options=Only&wormbase_rnai_phenotype_select_last=embryonic_lethal&wormbase_rnai_collection_phenotype_toggle=1&database=WormBaseRelease165__WS_CURRENT&default_link_last=wormbase_gene_id&wormbase_go_term_has_annotation_options_last=Only&collection_seq_scope_type=transcript_exon_intron&wormbase_go_term_has_annotation_options_filter=child_count&stage_initialised=start&stage_initialised=filter&stage_initialised=output&wormbase_go_term_has_annotation_options=Only&wormbase_rnai_has_phenotype_annotation_options_filter=phenotypinfo_observed&wormbase_go_term_goterm_type_last=biological_process&wormbase_rnai_author_options_last=abagyan_r&wormbase_rnai_has_annotation_options_last=Only&stage_prev=output&schema_last=WS_CURRENT&wormbase_gene_has_homology_options=Only&wormbase_rnai_has_phenotype_annotation_options=Only&wormbase_gene_collection_species_toggle=1&wormbase_gene_homolog_blastp_evalue_last=100&wormbase_rnai_author_options=abagyan_r&wormbase_gene_has_annotation_options=Only&wormbase_gene_collection_identity_status=1&wormbase_rnai_gene_count_options=1&wormbase_rnai_phenotype_status_options_last=Only&wormbase_rnai_has_experiment_options=Only&wormbase_go_term_goterm_id_list_options=go_term&wormbase_rnai_laboratory=aa&wormbase_gene_homology_shared_options=Only&wormbase_rnai_gene_count_options_last=1&dataset=wormbase_rnai&wormbase_go_term_goterm_type=biological_process&status_count_start=63640&wormbase_rnai_has_experiment_options_last=Only&wormbase_gene_species_selection_last=caenorhabditis_elegans&wormbase_rnai_phenotype_status_options_filter=rnai_phenotype_observed&wormbase_rnai_has_annotation_options_filter=has_paper&database_last=WormBaseRelease165__WS_CURRENT&wormbase_go_term_goterm_id_list_options_list=GO%3A0003673&status_count_output=-1 [HERE]],
+
*Click <span class="Apple-style-span" style="font-weight: bold;">&lt;Results&gt;</span> button&nbsp;to produce the results shown [http://www.wormbase.org/biomart/martview?VIRTUALSCHEMANAME=default&ATTRIBUTES=wormbase_rnai.default.attributes.rnai|wormbase_rnai.default.attributes.phenotype_observed_dminfo|wormbase_rnai.default.attributes.inhibits_gene_dminfo|wormbase_rnai.default.attributes.author_dmlist|wormbase_go_term.default.attributes.go_term|wormbase_go_term.default.attributes.term&FILTERS=wormbase_rnai.default.filters.phenotype_primary_name_options.%22embryonic_lethal%22&VISIBLEPANEL=resultspanel [HERE]].
−
**Click '''export''' to produce the results shown [http://www.wormbase.org/biomart/martview/martview?collection_rnai=rnai&collection_phenotype_summary=phenotype_observed_dminfo&collection_inhibits=inhibits_gene_dminfo&collection_experiment=author_dmlist&outformat=html&outcompress=none&stage=output&wormbase_rnai_phenotype_select=embryonic_lethal&wormbase_rnai_laboratory_last=aa&wormbase_gene_species_selection=caenorhabditis_elegans&schema=WS_CURRENT&default_link=wormbase_gene_id&outtype=feature_page&dataset_last=wormbase_rnai&wormbase_rnai_has_experiment_options_filter=experiment_author_count&wormbase_go_term_goterm_id_list_options_last=go_term&second_dataset=wormbase_go_term&wormbase_go_term_collection_goterm_id_list_toggle=1&wormbase_rnai_has_annotation_options=Only&wormbase_gene_homolog_blastp_evalue=100&seq_scope=tscr&status_count_filter=-1&wormbase_rnai_has_phenotype_annotation_options_last=Only&wormbase_rnai_phenotype_status_options=Only&wormbase_gene_rnai_phenotype_status_options=Only&wormbase_rnai_phenotype_select_last=embryonic_lethal&wormbase_rnai_collection_phenotype_toggle=1&database=WormBaseRelease165__WS_CURRENT&default_link_last=wormbase_gene_id&wormbase_go_term_has_annotation_options_last=Only&collection_seq_scope_type=transcript_exon_intron&wormbase_go_term_has_annotation_options_filter=child_count&stage_initialised=start&stage_initialised=filter&stage_initialised=output&wormbase_go_term_has_annotation_options=Only&wormbase_rnai_has_phenotype_annotation_options_filter=phenotypinfo_observed&wormbase_go_term_goterm_type_last=biological_process&wormbase_rnai_author_options_last=abagyan_r&wormbase_rnai_has_annotation_options_last=Only&stage_prev=output&schema_last=WS_CURRENT&wormbase_gene_has_homology_options=Only&wormbase_rnai_has_phenotype_annotation_options=Only&wormbase_gene_collection_species_toggle=1&wormbase_gene_homolog_blastp_evalue_last=100&wormbase_rnai_author_options=abagyan_r&wormbase_gene_has_annotation_options=Only&wormbase_gene_collection_identity_status=1&wormbase_rnai_gene_count_options=1&wormbase_rnai_phenotype_status_options_last=Only&wormbase_rnai_has_experiment_options=Only&wormbase_go_term_goterm_id_list_options=go_term&wormbase_rnai_laboratory=aa&wormbase_gene_homology_shared_options=Only&wormbase_rnai_gene_count_options_last=1&dataset=wormbase_rnai&wormbase_go_term_goterm_type=biological_process&status_count_start=63640&wormbase_rnai_has_experiment_options_last=Only&wormbase_gene_species_selection_last=caenorhabditis_elegans&wormbase_rnai_phenotype_status_options_filter=rnai_phenotype_observed&wormbase_rnai_has_annotation_options_filter=has_paper&database_last=WormBaseRelease165__WS_CURRENT&wormbase_go_term_goterm_id_list_options_list=GO%3A0003673&status_count_output=-1&_export=1 [HERE]].
 
  
 
[[Data mining:WormMart:Example 2|&lt;-Last]] ... [[Data mining:WormMart|Index of Examples]]
 
[[Data mining:WormMart:Example 2|&lt;-Last]] ... [[Data mining:WormMart|Index of Examples]]

Revision as of 13:50, 21 May 2008

Download the set of all RNAi experiments that resulted in an embryonic lethal (Emb) phenotype, and in which the target genes are classified as serine/threonine kinases.

  • Start a new WormMart query and;
    • Select the latest database and the RNAi dataset
  • Within the Filter section;
    • Under Phenotype, Enable the Limit to Phenotype Primary Name filter, and select the embryonic lethal option,
  • Within the lower Dataset section;
    • For the Second Dataset select GO Term as we will use this dataset to filter for serine/threonone kinases,
    • Within the Go Term's Filter section, Enable the Limit to GO Term ID(s) filter, and enter GO:0004674 (protein serine/threonine kinase activity). 


  • Within the RNAi Attribute section;
    • In the RNAi section, select RNAi WB ID,
    • In the Phenotype section, select Observed Phen Info (merged),
    • In the Inhibits Gene section, select Gene Info (merged),
    • In the Experiment section, select Author (merged)
  • Click <Results> button to produce the results shown [HERE].

<-Last ... Index of Examples

Retrieved from "https://wiki.wormbase.org/index.php?title=Data_mining:WormMart:Example_3&oldid=1169"