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| − | === Example 2: From all genes in C.elegans that have an ortholog in C. briggsae, are located in chromosome III, have an observed larval lethal phenotype in an RNAi screen, and have annotated UTRs, provide a FASTA file containing peptide sequence === | + | === Example 2: From all genes in C.elegans that have an ortholog in C. briggsae, are located in chromosome III, have an observed larval lethal phenotype in an RNAi screen, and have annotated UTRs, provide a FASTA file containing peptide sequence === |
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| − | * Start a new WormMart query and; | + | *Start a new [http://www.wormbase.org/biomart/martview WormMart] query and; |
| − | ** Select the '''Gene''' dataset. | + | **Select the latest database and the '''Gene''' dataset. |
| − | ** Click '''<next>''' to proceed to the '''FILTER''' page. | + | *Within the <span class="Apple-style-span" style="font-weight: bold;">Filter</span> section; |
| − | * On the FILTER page;
| + | **In the '''Location''' section, enable the '''Chromosome''' filter, and set to <span class="Apple-style-span" style="font-weight: bold;">C.elegans Chr III</span>,<br> |
| − | ** In the '''Identification''' section, enable the '''Limit to Species''' filter, and set to '''Caenorhabditis elegans''',
| + | **In the '''Homologs/Orthologs''' section; |
| − | ** In the '''Location''' section, enable the '''Limit to Chromosome''' filter, and set to '''III''', | + | ***enable the '''Homologs in Species''' filter and set to '''Caenorhabditis briggsae''', |
| − | ** In the '''Homologs/Orthologs''' section; | + | ***enable the '''Homologs which share''' filter and set to '''Compara Ortholog, Only''' |
| − | *** enable the '''Homologs in Species''' filter and set to '''Caenorhabditis briggsae''', | + | **In the <span class="Apple-style-span" style="font-weight: bold;">Phenotype</span> section,<br> |
| − | *** enable the '''Homologs which share''' filter and set to '''Compara Ortholog, Only''' | + | ***enable '''[Function] RNAi Phenotypes that are''' set to '''Scored for and observed, Only''' |
| − | ** In the '''Annotation''' section, <br /> | + | **enable '''[Function] RNAi phenotype''' and set to '''larval_lethal''' |
| − | *** enable '''[Transcript] UTR annotation''' and set to '''UTR5+UTR3''', | + | **In the '''Annotation''' section, <br> |
| − | *** enable '''[Function] RNAi phenotype''' and set to '''LVL larval_lethal'''
| + | ***enable '''[Transcript] UTR annotation''' and set to '''UTR5+UTR3''', |
| − | *** enable '''[FUNCTION] RNAi Phenotypes that are''' set to '''Scored for and observed, Only''' | |
| − | ** The above selection is shown [http://www.wormbase.org/biomart/martview/martview?wormbase_gene_collection_species_toggle=1&wormbase_gene_species_selection=caenorhabditis_elegans&wormbase_gene_species_selection_last=caenorhabditis_elegans&wormbase_gene_gene_class=aak&wormbase_gene_gene_class_last=aak&wormbase_gene_collection_chromosome_name_toggle=1&wormbase_gene_chromosome_name=iii&wormbase_gene_chromosome_name_last=iii&wormbase_gene_chromosome_strand=-1&wormbase_gene_chromosome_strand_last=-1&wormbase_gene_map_map=i&wormbase_gene_map_map_last=i&wormbase_gene_has_homology_options_filter=homology_group_cog_count&wormbase_gene_has_homology_options=Only&wormbase_gene_collection_homolog_species_toggle=1&wormbase_gene_homolog_species=caenorhabditis_briggsae&wormbase_gene_homolog_species_last=caenorhabditis_briggsae&wormbase_gene_homolog_blastp_rank=1&wormbase_gene_homolog_blastp_rank_last=1&wormbase_gene_homolog_blastp_evalue=100&wormbase_gene_homolog_blastp_evalue_last=100&wormbase_gene_collection_homolog_shared_toggle=1&wormbase_gene_homology_shared_options_filter=homolog_ortholog&wormbase_gene_homology_shared_options=Only&wormbase_gene_has_annotation_options_filter=has_concise_description&wormbase_gene_has_annotation_options=Only&wormbase_gene_collection_identity_status=1&wormbase_gene_identity_status=live&wormbase_gene_identity_status_last=live&wormbase_gene_history_action=acquires_merge&wormbase_gene_history_action_last=acquires_merge&wormbase_gene_prediction_status=confirmed&wormbase_gene_prediction_status_last=confirmed&wormbase_gene_coding_status=coding&wormbase_gene_coding_status_last=coding&wormbase_gene_collection_utr_status_toggle=1&wormbase_gene_utr_status=utr5%2Butr3&wormbase_gene_utr_status_last=utr5%2Butr3&wormbase_gene_collection_rnai_phenotype_toggle=1&wormbase_gene_rnai_phenotype_options=larval_lethal&wormbase_gene_rnai_phenotype_options_last=larval_lethal&wormbase_gene_collection_rnai_phenotype_status_toggle=1&wormbase_gene_rnai_phenotype_status_options_filter=rnai_observed_count&wormbase_gene_rnai_phenotype_status_options=Only&wormbase_gene_rnai_phenotype_observation_options=1&wormbase_gene_rnai_phenotype_observation_options_last=1&wormbase_gene_rnai_phenotype_specific_observation_options=1&wormbase_gene_rnai_phenotype_specific_observation_options_last=1&default_link=---&default_link_last=---&stage=filter&schema=WS_CURRENT&wormbase_gene_rnai_phenotype_status_options_last=Only&dataset_last=wormbase_gene&outformat=html&seq_scope=tscr&status_count_filter=81&wormbase_gene_annotation_list_options_last=operon&wormbase_gene_has_annotation_options_last=Only&outcompress=none&collection_genomic_position=chromosome_name&database=WormBaseRelease165__WS_CURRENT&wormbase_gene_id_list_options_last=gene&collection_seq_scope_type=transcript_exon_intron&stage_initialised=start&stage_initialised=filter&wormbase_gene_homology_list_options_last=homology_group_cog&stage_prev=filter&collection_homologs=homolog_species&schema_last=WS_CURRENT&wormbase_gene_has_homology_options_last=Only&dataset=wormbase_gene&status_count_start=44996&wormbase_gene_homology_shared_options_last=Only&database_last=WormBaseRelease165__WS_CURRENT [HERE]]. | |
| − | ** Click '''next''' to proceed to the '''OUTPUT''' page. | |
| | | | |
| − | * On the '''OUTPUT''' page, | + | *Within the <span class="Apple-style-span" style="font-weight: bold;">Attributes</span> section, |
| − | ** In the '''Select the Attribute Page''' section, select '''Gene, CDS and Protein Sequences''' option, | + | **Select '''Gene Sequences''' option, |
| − | ** In the '''SEQUENCES''' section, select '''Peptides''', | + | **In <span class="Apple-style-span" style="font-weight: bold;">Sequence Type</span>, select '''Peptides''', |
| − | ** In the '''Header Information, Molecular names''' section, select '''WB WormPep ID'''. | + | **In '''Header Attributes, Molecular names''', select '''WB WormPep ID'''. |
| − | ** The above selection is shown [http://www.wormbase.org/biomart/martview/martview?outtype=sequence&collection_seq_scope_type=peptide&upstream_flank=100&downstream_flank=100&collection_gene=gene&collection_gene=public_name&collection_molecular=protein&outformat=fasta&outcompress=none&stage=output&collection_seq_scope_type_this=wormbase_dna.transcript_exon_intron&wormbase_gene_gene_class_last=aak&wormbase_gene_species_selection=caenorhabditis_elegans&wormbase_gene_chromosome_name=iii&wormbase_gene_rnai_phenotype_observation_options_last=1&schema=WS_CURRENT&wormbase_gene_homolog_species=caenorhabditis_briggsae&default_link=---&wormbase_gene_rnai_phenotype_status_options_last=Only&wormbase_gene_chromosome_strand=-1&dataset_last=wormbase_gene&wormbase_gene_chromosome_name_last=iii&wormbase_gene_utr_status=utr5%2Butr3&wormbase_gene_has_homology_options_filter=homology_group_cog_count&wormbase_gene_homolog_blastp_evalue=100&wormbase_gene_prediction_status=confirmed&seq_scope=tscr&status_count_filter=81&wormbase_gene_history_action=acquires_merge&wormbase_gene_homology_shared_options_filter=homolog_ortholog&wormbase_gene_has_annotation_options_last=Only&wormbase_gene_rnai_phenotype_observation_options=1&wormbase_gene_coding_status_last=coding&wormbase_gene_collection_homolog_shared_toggle=1&wormbase_gene_homolog_blastp_rank_last=1&collection_genomic_position=chromosome_name&wormbase_gene_rnai_phenotype_status_options=Only&wormbase_gene_prediction_status_last=confirmed&wormbase_gene_history_action_last=acquires_merge&wormbase_gene_rnai_phenotype_specific_observation_options_last=1&wormbase_gene_map_map_last=i&database=WormBaseRelease165__WS_CURRENT&wormbase_gene_chromosome_strand_last=-1&wormbase_gene_collection_chromosome_name_toggle=1&default_link_last=---&wormbase_gene_collection_rnai_phenotype_toggle=1&wormbase_gene_has_annotation_options_filter=has_concise_description&wormbase_gene_rnai_phenotype_specific_observation_options=1&wormbase_gene_collection_homolog_species_toggle=1&collection_gene_id=gene&collection_gene_id=public_name&stage_initialised=start&stage_initialised=filter&stage_initialised=output&wormbase_gene_identity_status=live&wormbase_gene_collection_utr_status_toggle=1&wormbase_gene_collection_rnai_phenotype_status_toggle=1&stage_prev=output&collection_homologs=homolog_species&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_map_map=i&wormbase_gene_rnai_phenotype_options_last=larval_lethal&wormbase_gene_rnai_phenotype_options=larval_lethal&wormbase_gene_has_annotation_options=Only&wormbase_gene_coding_status=coding&wormbase_gene_collection_identity_status=1&wormbase_gene_rnai_phenotype_status_options_filter=rnai_observed_count&wormbase_gene_identity_status_last=live&wormbase_gene_utr_status_last=utr5%2Butr3&wormbase_gene_gene_class=aak&wormbase_gene_has_homology_options_last=Only&wormbase_gene_homolog_blastp_rank=1&wormbase_gene_homolog_species_last=caenorhabditis_briggsae&wormbase_gene_homology_shared_options=Only&dataset=wormbase_gene&status_count_start=44996&wormbase_gene_species_selection_last=caenorhabditis_elegans&status_count_output=81&wormbase_gene_homology_shared_options_last=Only&database_last=WormBaseRelease165__WS_CURRENT [HERE]]. | + | **Click the <span class="Apple-style-span" style="font-weight: bold; "><Results></span> button to run the query.<br> |
| − | ** Click '''export''' to run the query.
| + | **The results are shown [http://www.biomart.org/biomart/martview?VIRTUALSCHEMANAME=default&ATTRIBUTES=wormbase_gene.default.sequence.gene|wormbase_gene.default.sequence.public_name|wormbase_gene.default.sequence.peptide|wormbase_gene.default.sequence.protein&FILTERS=wormbase_gene.default.filters.species_selection.%22Caenorhabditis%20elegans%22|wormbase_gene.default.filters.homolog_species.%22Caenorhabditis%20briggsae%22|wormbase_gene.default.filters.chromosome_name.%22III%22|wormbase_gene.default.filters.identity_status.%22Live%22|wormbase_gene.default.filters.rnai_phenotype_options.%22larval_lethal%22|wormbase_gene.default.filters.homolog_ortholog.only&VISIBLEPANEL=resultspanel [HERE]]. |
| − | ** The results are shown [http://www.wormbase.org/biomart/martview/martview?outtype=sequence&collection_seq_scope_type=peptide&upstream_flank=100&downstream_flank=100&collection_gene=gene&collection_gene=public_name&collection_molecular=protein&outformat=fasta&outcompress=none&stage=output&collection_seq_scope_type_this=wormbase_dna.transcript_exon_intron&wormbase_gene_gene_class_last=aak&wormbase_gene_species_selection=caenorhabditis_elegans&wormbase_gene_chromosome_name=iii&wormbase_gene_rnai_phenotype_observation_options_last=1&schema=WS_CURRENT&wormbase_gene_homolog_species=caenorhabditis_briggsae&default_link=---&wormbase_gene_rnai_phenotype_status_options_last=Only&wormbase_gene_chromosome_strand=-1&dataset_last=wormbase_gene&wormbase_gene_chromosome_name_last=iii&wormbase_gene_utr_status=utr5%2Butr3&wormbase_gene_has_homology_options_filter=homology_group_cog_count&wormbase_gene_homolog_blastp_evalue=100&wormbase_gene_prediction_status=confirmed&seq_scope=tscr&status_count_filter=81&wormbase_gene_history_action=acquires_merge&wormbase_gene_homology_shared_options_filter=homolog_ortholog&wormbase_gene_has_annotation_options_last=Only&wormbase_gene_rnai_phenotype_observation_options=1&wormbase_gene_coding_status_last=coding&wormbase_gene_collection_homolog_shared_toggle=1&wormbase_gene_homolog_blastp_rank_last=1&collection_genomic_position=chromosome_name&wormbase_gene_rnai_phenotype_status_options=Only&wormbase_gene_prediction_status_last=confirmed&wormbase_gene_history_action_last=acquires_merge&wormbase_gene_rnai_phenotype_specific_observation_options_last=1&wormbase_gene_map_map_last=i&database=WormBaseRelease165__WS_CURRENT&wormbase_gene_chromosome_strand_last=-1&wormbase_gene_collection_chromosome_name_toggle=1&default_link_last=---&wormbase_gene_collection_rnai_phenotype_toggle=1&wormbase_gene_has_annotation_options_filter=has_concise_description&wormbase_gene_rnai_phenotype_specific_observation_options=1&wormbase_gene_collection_homolog_species_toggle=1&collection_gene_id=gene&collection_gene_id=public_name&stage_initialised=start&stage_initialised=filter&stage_initialised=output&wormbase_gene_identity_status=live&wormbase_gene_collection_utr_status_toggle=1&wormbase_gene_collection_rnai_phenotype_status_toggle=1&stage_prev=output&collection_homologs=homolog_species&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_map_map=i&wormbase_gene_rnai_phenotype_options_last=larval_lethal&wormbase_gene_rnai_phenotype_options=larval_lethal&wormbase_gene_has_annotation_options=Only&wormbase_gene_coding_status=coding&wormbase_gene_collection_identity_status=1&wormbase_gene_rnai_phenotype_status_options_filter=rnai_observed_count&wormbase_gene_identity_status_last=live&wormbase_gene_utr_status_last=utr5%2Butr3&wormbase_gene_gene_class=aak&wormbase_gene_has_homology_options_last=Only&wormbase_gene_homolog_blastp_rank=1&wormbase_gene_homolog_species_last=caenorhabditis_briggsae&wormbase_gene_homology_shared_options=Only&dataset=wormbase_gene&status_count_start=44996&wormbase_gene_species_selection_last=caenorhabditis_elegans&status_count_output=81&wormbase_gene_homology_shared_options_last=Only&database_last=WormBaseRelease165__WS_CURRENT&_export=1 [HERE]]. | |
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| − | [[Data_mining:WormMart:Example_1|<-Last]] ... [[Data_mining:WormMart|Index of Examples]] ... [[Data_mining:WormMart:Example_3|Next->]] | + | [[Data mining:WormMart:Example 1|<-Last]] ... [[Data mining:WormMart|Index of Examples]] ... [[Data mining:WormMart:Example 3|Next->]] |
