Difference between revisions of "Data mining:WormMart:Example 6"
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(second Dataset Filters-><span style="display: inline;">Identification-></span>[Anatomy Term] ID(s)->Browse to upload the file anatomy_terms (a list of IDs only).<br><br>5. find any gene that is in gene list 3 but not in gene list 4.<br><br>as of WS189, this results in four genes WBGene00000548 (removed in WS190), WBGene00003168, WBGene00003471, WBGene00003179<br> | (second Dataset Filters-><span style="display: inline;">Identification-></span>[Anatomy Term] ID(s)->Browse to upload the file anatomy_terms (a list of IDs only).<br><br>5. find any gene that is in gene list 3 but not in gene list 4.<br><br>as of WS189, this results in four genes WBGene00000548 (removed in WS190), WBGene00003168, WBGene00003471, WBGene00003179<br> | ||
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Revision as of 18:42, 11 August 2010
1. get a list of terms that include "touch receptor neuron" and all
children terms.
2. get a list of all anatomy terms
<http://www.wormbase.org/biomart/martview?VIRTUALSCHEMANAME=default&ATTRIBUTES=wormbase_anatomy_term.default.attributes.anatomy_term>
remove the 9 terms from above, save as anatomy_terms (lines of anatomy term ID ONLY).
3. get a list of all 'live' Ce genes, 2nd dataset of anatomy term "touch
receptor neuron" incl. child terms.
<http://www.wormbase.org/biomart/martview?VIRTUALSCHEMANAME=default&FILTERS=wormbase_anatomy_term.default.filters.anatomy_term_ancestor_options."touch receptor neuron"|wormbase_gene.default.filters.identity_status."Live"|wormbase_gene.default.filters.species_selection."Caenorhabditis elegans"&ATTRIBUTES=wormbase_anatomy_term.default.attributes.anatomy_term|wormbase_gene.default.attributes.gene>
4. get a list of all 'live' Ce genes, 2nd dataset of anatomy terms in
anatomy_terms
(second Dataset Filters->Identification->[Anatomy Term] ID(s)->Browse to upload the file anatomy_terms (a list of IDs only).
5. find any gene that is in gene list 3 but not in gene list 4.
as of WS189, this results in four genes WBGene00000548 (removed in WS190), WBGene00003168, WBGene00003471, WBGene00003179
