Difference between revisions of "Data mining:WormMart:Example 3"
From WormBaseWiki
Jump to navigationJump to search| Line 1: | Line 1: | ||
| − | === 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. === | + | === 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 | + | *Start a new [http://www.wormbase.org/biomart/martview WormMart] query and; |
| − | + | **Select the latest database and the '''RNAi''' dataset<br> | |
| − | ** | ||
| − | * | + | *Within the <span class="Apple-style-span" style="font-weight: bold;">Filter</span> section; |
| − | ** | + | **Under '''Phenotype Annotation''', Enable the '''Phenotype Inc. Descendents''' 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,<br> | |
| − | |||
| − | |||
| − | * ** 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 [http://www.ebi.ac.uk/ego/DisplayGoTerm?id=GO:0003673&selected=GO:0003673&viz=tree [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 [http://www.ebi.ac.uk/ego/DisplayGoTerm?id=GO:0003673&selected=GO:0003673&viz=tree [HERE]] |
| − | ** Type the search term ''' serine threonine kinase''' into the '''Search''' box, and click '''<Search GO>''', which brings you [http://www.ebi.ac.uk/ego/GSearch?query=serine+threonine+kinase&mode=name_syno&ontology=all_ont [HERE]] | + | **Type the search term '''serine threonine kinase''' into the '''Search''' box, and click '''<Search GO>''', which brings you [http://www.ebi.ac.uk/ego/GSearch?query=serine+threonine+kinase&mode=name_syno&ontology=all_ont [HERE]] |
| − | ** Looking through the result list, '''GO:0004674 (protein serine/threonine kinase activity)''' seems best, | + | **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, | + | **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 [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]], | + | **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]], |
| − | ** Click '''<next>''' to proceed to the '''OUTPUT''' page. | + | **Click '''<next>''' to proceed to the '''OUTPUT''' page. |
| − | * On the OUTPUT page; | + | *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)''', |
| − | ** 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]], | + | **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 '''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]]. | + | **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|<-Last]] ... [[Data mining:WormMart|Index of Examples]] |
Revision as of 13:33, 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
- Select the latest database and the RNAi dataset
- Within the Filter section;
- Under Phenotype Annotation, Enable the Phenotype Inc. Descendents 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,
- For the Second Dataset select GO Term as we will use this dataset to filter for serine/threonone kinases,
- 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;
