Data mining:WormMart:Example 3

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 RNAi dataset as shown [HERE]
  • Click <next> to proceed to the FILTER page.

• On the FILTER page;
  • In the Phenotype section, Enable the Limit to Phenotype filter, and select the [Emb] embryonic lethal option,
  • In the Select the second dataset section;
    • For the Second Dataset select GO Term as we will use this dataset to filter for serine/threonone kinases,
    • For Link Dataset Via select Genes,
  • The page will auto-reload with the GO Term dataset filters at the bottom of the page, 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_gene_species_selection=caenorhabditis_elegans&schema=WS_CURRENT&dataset_last=wormbase_rnai&outformat=html&wormbase_gene_homolog_blastp_evalue=100&seq_scope=tscr&stage=filter&outcompress=none&wormbase_gene_rnai_phenotype_status_options=Only&database=WormBaseRelease165__WS_CURRENT&collection_seq_scope_type=transcript_exon_intron&stage_initialised=start&stage_initialised=filter&stage_prev=filter&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_gene_homology_shared_options=Only&dataset=wormbase_rnai&status_count_start=63640&wormbase_gene_species_selection_last=caenorhabditis_elegans&database_last=WormBaseRelease165__WS_CURRENT&wormbase_rnai_rnai_list_options_last=rnai&wormbase_rnai_has_phenotype_annotation_options_last=Only&wormbase_rnai_phenotype_status_options_last=Only&wormbase_rnai_Inhibits_list_options_last=gene&wormbase_rnai_has_experiment_options_last=Only&wormbase_rnai_has_annotation_options_last=Only&wormbase_rnai_citation_options_last=paper&wormbase_go_term_has_annotation_options=Only [HERE],

• ** In the 2'nd dataset Identification:Limit to GO Term ID(s) section, click the <browse> button to bring up a GO Term search page [HERE]
  • Type the search term serine threonine kinase into the Search box, and click <Search GO>, which brings you [HERE]
  • Looking through the result list, GO:0004674 (protein serine/threonine kinase activity) seems best,
  • Back on the MartView FILTER page, Enable the Limit to GO Term ID(s) filter, and paste GO:0004674 into the text box,
  • The above selection is shown [HERE],
  • Click <next> to proceed to the OUTPUT page.

• On the OUTPUT page;
  • 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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