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

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*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;  
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**Under&nbsp;'''Phenotype Annotation''', Enable the '''Phenotype Inc. Descendents'''&nbsp;filter, and select the '''embryonic lethal''' option,
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**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;  
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**For the '''Second Dataset''' select '''GO Term''' as we will use this dataset to filter for serine/threonone kinases,<br>
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**For the '''Second Dataset''' select '''GO Term''' as we will use this dataset to filter for serine/threonone kinases,
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**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;">
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</span>
  
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*** In the 2'nd dataset '''Identification:Limit to GO Term ID(s)''' section, click the '''&lt;browse&gt;''' button to bring up a GO Term search page [http://www.ebi.ac.uk/ego/DisplayGoTerm?id=GO:0003673&selected=GO:0003673&viz=tree [HERE]]
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*Within the RNAi <span class="Apple-style-span" style="font-weight: bold;">Attribute</span>&nbsp;section;  
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**Type the search term '''serine threonine kinase''' into the '''Search''' box, and click '''&lt;Search GO&gt;''', which brings you [http://www.ebi.ac.uk/ego/GSearch?query=serine+threonine+kinase&mode=name_syno&ontology=all_ont [HERE]]
 
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**Looking through the result list, '''GO:0004674 (protein serine/threonine kinase activity)''' seems best,
 
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**Back on the MartView '''FILTER''' page, Enable the '''Limit to GO Term ID(s)''' filter, and paste '''GO:0004674''' into the text box,
 
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**The above selection is shown [http://www.wormbase.org/biomart/martview/martview?wormbase_rnai_has_phenotype_annotation_options_filter=phenotypinfo_observed&wormbase_rnai_has_phenotype_annotation_options=Only&wormbase_rnai_collection_phenotype_toggle=1&wormbase_rnai_phenotype_select=embryonic_lethal&wormbase_rnai_phenotype_select_last=embryonic_lethal&wormbase_rnai_phenotype_status_options_filter=rnai_phenotype_observed&wormbase_rnai_phenotype_status_options=Only&wormbase_rnai_gene_count_options=1&wormbase_rnai_gene_count_options_last=1&wormbase_rnai_has_experiment_options_filter=experiment_author_count&wormbase_rnai_has_experiment_options=Only&wormbase_rnai_author_options=abagyan_r&wormbase_rnai_author_options_last=abagyan_r&wormbase_rnai_laboratory=aa&wormbase_rnai_laboratory_last=aa&wormbase_rnai_has_annotation_options_filter=has_paper&wormbase_rnai_has_annotation_options=Only&second_dataset=wormbase_go_term&default_link=wormbase_gene_id&default_link_last=wormbase_gene_id&wormbase_go_term_goterm_type=biological_process&wormbase_go_term_goterm_type_last=biological_process&wormbase_go_term_collection_goterm_id_list_toggle=1&wormbase_go_term_goterm_id_list_options=go_term&wormbase_go_term_goterm_id_list_options_list=GO%3A0003673&wormbase_go_term_has_annotation_options_filter=child_count&wormbase_go_term_has_annotation_options=Only&stage=filter&wormbase_gene_species_selection=caenorhabditis_elegans&schema=WS_CURRENT&dataset_last=wormbase_rnai&outformat=html&wormbase_gene_homolog_blastp_evalue=100&seq_scope=tscr&status_count_filter=-1&wormbase_rnai_has_phenotype_annotation_options_last=Only&wormbase_rnai_rnai_list_options_last=rnai&outcompress=none&wormbase_gene_rnai_phenotype_status_options=Only&database=WormBaseRelease165__WS_CURRENT&wormbase_rnai_Inhibits_list_options_last=gene&wormbase_go_term_has_annotation_options_last=Only&collection_seq_scope_type=transcript_exon_intron&stage_initialised=start&stage_initialised=filter&wormbase_rnai_has_annotation_options_last=Only&stage_prev=filter&wormbase_rnai_citation_options_last=paper&schema_last=WS_CURRENT&wormbase_gene_has_homology_options=Only&wormbase_gene_collection_species_toggle=1&wormbase_gene_homolog_blastp_evalue_last=100&wormbase_gene_has_annotation_options=Only&wormbase_gene_collection_identity_status=1&wormbase_rnai_phenotype_status_options_last=Only&wormbase_gene_homology_shared_options=Only&dataset=wormbase_rnai&wormbase_rnai_has_experiment_options_last=Only&status_count_start=63640&wormbase_gene_species_selection_last=caenorhabditis_elegans&database_last=WormBaseRelease165__WS_CURRENT&wormbase_go_term_goterm_id_list_options_last=go_term&wormbase_go_term_annotation_list_options_last=gene [HERE]],
 
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**Click '''&lt;next&gt;''' to proceed to the '''OUTPUT''' page.
 
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*On the OUTPUT page;  
 
 
**In the '''RNAi''' section, select '''RNAi WB ID''',  
 
**In the '''RNAi''' section, select '''RNAi WB ID''',  
 
**In the '''Phenotype''' section, select '''Observed Phen Info (merged)''',  
 
**In the '''Phenotype''' section, select '''Observed Phen Info (merged)''',  

Revision as of 13:45, 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)
    • The above selection is shown [HERE],
    • Click export to produce the results shown [HERE].

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