Difference between revisions of "Data mining:WormMart:Example 3"
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=== 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 [http:// | + | *Start a new [http://caprica.caltech.edu:9002/biomart/martview WormMart] query and; |
**Select the latest database and the '''RNAi''' dataset<br> | **Select the latest database and the '''RNAi''' dataset<br> | ||
*Within the <span class="Apple-style-span" style="font-weight: bold;">Filter</span> section; | *Within the <span class="Apple-style-span" style="font-weight: bold;">Filter</span> section; | ||
| − | **Under '''Phenotype''', Enable the | + | **Under '''Phenotype''', Enable the '''Limit to Phenotype Primary Name''' filter, and select the '''embryonic lethal''' option, |
*Within the lower '''Dataset''' section; | *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, | ||
**Within the Go Term's <span class="Apple-style-span" style="font-weight: bold;">Filter</span> section, Enable the '''Limit to GO Term ID(s)''' filter, and enter <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>. </span><span class="Apple-style-span" style="font-weight: bold;"> | **Within the Go Term's <span class="Apple-style-span" style="font-weight: bold;">Filter</span> section, Enable the '''Limit to GO Term ID(s)''' filter, and enter <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>. </span><span class="Apple-style-span" style="font-weight: bold;"> | ||
</span> | </span> | ||
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*Within the RNAi <span class="Apple-style-span" style="font-weight: bold;">Attribute</span> section; | *Within the RNAi <span class="Apple-style-span" style="font-weight: bold;">Attribute</span> section; | ||
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**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)''' | ||
| − | *Click <span class="Apple-style-span" style="font-weight: bold;"><Results></span> button to produce the results shown [http:// | + | *Click <span class="Apple-style-span" style="font-weight: bold;"><Results></span> button to produce the results shown [http://caprica.caltech.edu:9002/biomart/martview?VIRTUALSCHEMANAME=default&ATTRIBUTES=wormbase_rnai.default.attributes.rnai|wormbase_rnai.default.attributes.phenotype_observed_dminfo|wormbase_rnai.default.attributes.inhibits_gene_dminfo|wormbase_rnai.default.attributes.author_dmlist|wormbase_go_term.default.attributes.go_term|wormbase_go_term.default.attributes.term&FILTERS=wormbase_rnai.default.filters.phenotype_primary_name_options.%22embryonic_lethal%22&VISIBLEPANEL=resultspanel [HERE]]. |
[[Data mining:WormMart:Example 2|<-Last]] ... [[Data mining:WormMart|Index of Examples]] | [[Data mining:WormMart:Example 2|<-Last]] ... [[Data mining:WormMart|Index of Examples]] | ||
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| + | [[Category:User Guide]] | ||
Latest revision as of 10:42, 31 January 2013
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, 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)
- Click <Results> button to produce the results shown [HERE].
