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Cow-Human Ortholog Pathways and Gene annotations for QTL Phenotype

Created: 2007-10-03 18:36:00      Last updated: 2009-12-03 16:16:31

This workflow searches for genes which reside in a QTL (Quantitative Trait Loci) region in the cow, Bos taurus. The workflow requires an input of: a chromosome name or number; a QTL start base pair position; QTL end base pair position. Data is then extracted from BioMart to annotate each of the genes found in this region. As the Cow genome is currently unfinished, the workflow subsequently maps the cow ensembl gene ids to human orthologues. Entrez and UniProt identifiers are then identified and sent to KEGG to obtain KEGG gene identifiers. The KEGG gene identifiers are then used to searcg for pathways in the KEGG pathway database.

Example input:

chromosome_name: 17

start_position: 58127155

end_position: 68127155

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  • Friday 20 June 2008 15:13:40 (UTC)

    Do you have some kind of description and sample input data for this workflow..? :-)




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Workflow qtl_pathway_3.xml (1)

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No description

Created: 2008-07-12 | Last updated: 2008-07-12

Credits: User Paul Fisher

Workflow Pathways and Gene annotations for QTL region (1)

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This workflow searches for genes which reside in a QTL (Quantitative Trait Loci) region in rice, Oryza sativa. The workflow requires an input of: a chromosome name or number; a QTL start base pair position; QTL end base pair position. Data is then extracted from BioMart to annotate each of the genes found in this region. The Entrez and UniGene identifiers are then sent to KEGG to obtain KEGG gene identifiers. The KEGG gene identifiers are then used to searcg for pathways in the KEGG pathway d...

Created: 2011-05-27 | Last updated: 2011-05-27

Credits: User Paul Fisher