Difference between revisions of "Data mining:WormMart:Example 2"

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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  ===
  
*Start a new [http://www.wormbase.org/biomart/martview WormMart] query and;  
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*Start a new [http://caprica.caltech.edu:9002/biomart/martview/ WormMart] query and;  
 
**Select the latest database and the '''Gene''' dataset.  
 
**Select the latest database and the '''Gene''' dataset.  
 
*Within the <span class="Apple-style-span" style="font-weight: bold;">Filter</span>&nbsp;section;  
 
*Within the <span class="Apple-style-span" style="font-weight: bold;">Filter</span>&nbsp;section;  
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**In&nbsp;'''Header Attributes, Molecular names''', select '''WB WormPep ID'''.  
 
**In&nbsp;'''Header Attributes, Molecular names''', select '''WB WormPep ID'''.  
 
**Click the&nbsp;<span class="Apple-style-span" style="font-weight: bold;">&lt;Results&gt;</span>&nbsp;button to run the query.<br>  
 
**Click the&nbsp;<span class="Apple-style-span" style="font-weight: bold;">&lt;Results&gt;</span>&nbsp;button to run the query.<br>  
**The results are shown [http://www.wormbase.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]].
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**The results are shown [http://caprica.caltech.edu:9002/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]].
  
 
[[Data mining:WormMart:Example 1|&lt;-Last]] ... [[Data mining:WormMart|Index of Examples]] ... [[Data mining:WormMart:Example 3|Next-&gt;]]
 
[[Data mining:WormMart:Example 1|&lt;-Last]] ... [[Data mining:WormMart|Index of Examples]] ... [[Data mining:WormMart:Example 3|Next-&gt;]]
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[[Category:User Guide]]

Latest revision as of 10:42, 31 January 2013

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

  • Start a new WormMart query and;
    • Select the latest database and the Gene dataset.
  • Within the Filter section;
    • In the Location section, enable the Chromosome filter, and set to C.elegans Chr III,
    • In the Homologs/Orthologs section;
      • enable the Homologs in Species filter and set to Caenorhabditis briggsae,
      • enable the Homologs which share filter and set to Compara Ortholog, Only
    • In the Phenotype section,
      • enable [Function] RNAi Phenotypes that are set to Scored for and observed, Only
    • enable [Function] RNAi phenotype and set to larval_lethal
    • In the Annotation section,
      • enable [Transcript] UTR annotation and set to UTR5+UTR3,
  • Within the Attributes section,
    • Select Gene Sequences option,
    • In Sequence Type, select Peptides,
    • In Header Attributes, Molecular names, select WB WormPep ID.
    • Click the <Results> button to run the query.
    • The results are shown [HERE].

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