Difference between revisions of "Data mining:WormMart"
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== Introduction == | == Introduction == | ||
| − | WormMart (http:// | + | WormMart (http://caprica.caltech.edu:9002/biomart/martview/) provides easy and interactive access to data en masse. In particular, WormMart enables users to retrieve sequences and genome annotations using a variety of filters to constrain retrieved results. Filters include such things as genomic location and the presence or absence of specific annotations. Data can be returned in a variety of formats, inluding HTML, text, FASTA, and even Microsoft Excel. It is expected that WormMart will eventually replace the [http://www.wormbase.org/db/searches/batch_genes Batch Genes] and [http://www.wormbase.org/db/searches/advanced/dumper Batch Sequences] pages. |
WormMart is the WormBase implementation of BioMart. Read more about BioMart at its [http://www.biomart.org official home page]. | WormMart is the WormBase implementation of BioMart. Read more about BioMart at its [http://www.biomart.org official home page]. | ||
| − | == WormMart | + | == WormMart Video Tutorial == |
| − | + | http://www.youtube.com/watch?v=BrbMAbxUseo | |
| − | + | == WormMart Worked Examples == | |
| − | * [[ | + | *[[Data mining:WormMart:Example 1|Example 1]] List all synonyms for the following genes; bli-1, egl-43, lag-1. |
| − | * [[ | + | *[[Data mining:WormMart:Example 2|Example 2]] From all genes in C.elegans that have an ortholog in C. briggsae, are located in chromosome III, are sterile in an RNAi screen, and have annotated UTRs, provide a FASTA file containing peptide sequence. |
| − | * [[ | + | *[[Data mining:WormMart:Example 3|Example 3]] Download the set of all RNAi experiments that resulted in an Emb phenotype, and in which the target genes are classified as serine/threonine kinases. |
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| + | *[[Data mining:WormMart:Example 4|Example 4]] Retrieve 1.5 kb promoter region upstream of a bunch of genes. | ||
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| + | *[[Data mining:WormMart:Example 5|Example 5]] How do I retrieve a list of transcription factors which when mutated or targeted by RNAi cause embryonic lethal phenotype? | ||
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| + | *[[Data mining:WormMart:Example 6|Example 6]] What genes are EXCLUSIVELY expressed in touch cell neurons? | ||
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| + | [[Category:User Guide]] | ||
Latest revision as of 10:40, 31 January 2013
Introduction
WormMart (http://caprica.caltech.edu:9002/biomart/martview/) provides easy and interactive access to data en masse. In particular, WormMart enables users to retrieve sequences and genome annotations using a variety of filters to constrain retrieved results. Filters include such things as genomic location and the presence or absence of specific annotations. Data can be returned in a variety of formats, inluding HTML, text, FASTA, and even Microsoft Excel. It is expected that WormMart will eventually replace the Batch Genes and Batch Sequences pages.
WormMart is the WormBase implementation of BioMart. Read more about BioMart at its official home page.
WormMart Video Tutorial
http://www.youtube.com/watch?v=BrbMAbxUseo
WormMart Worked Examples
- Example 1 List all synonyms for the following genes; bli-1, egl-43, lag-1.
- Example 2 From all genes in C.elegans that have an ortholog in C. briggsae, are located in chromosome III, are sterile in an RNAi screen, and have annotated UTRs, provide a FASTA file containing peptide sequence.
- Example 3 Download the set of all RNAi experiments that resulted in an Emb phenotype, and in which the target genes are classified as serine/threonine kinases.
- Example 4 Retrieve 1.5 kb promoter region upstream of a bunch of genes.
- Example 5 How do I retrieve a list of transcription factors which when mutated or targeted by RNAi cause embryonic lethal phenotype?
- Example 6 What genes are EXCLUSIVELY expressed in touch cell neurons?
