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Pathways and Gene annotations for QTL region

Created: 2009-11-19 18:18:52      Last updated: 2012-09-07 18:23:36

This workflow searches for genes which reside in a QTL (Quantitative Trait Loci) region in the mouse, Mus musculus. 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 UniProt 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 database.

Example input:

chromosome_name: 17

start_position: 28500000

end_position: 32500000

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Information Workflow Components

Inputs (3)
Processors (42)
Beanshells (11)
Outputs (9)
Links (63)
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Taverna 1

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Citations (1)

1. Fisher P, Hedeler C, Wolstencroft K, Hulme H, Noyes H, Kemp S, Stevens R, Brass A, A systematic strategy for large-scale analysis of genotype phenotype correlations: identification of candidate genes involved in African trypanosomiasis, Nucleic Acids Research, 20 August 2007, http://nar.oxfordjournals.org/cgi/content/full/35/16/5625


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Reviews Reviews (1)

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Review Title: asdlfkj

Rating: 5 out of 5

Created: 2011-12-01 07:21:30 | Updated: 2011-12-01 07:54:00

 lasdf

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Comments Comments (8)

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  • Friday 20 June 2008 15:14:48 (UTC)

    Do you have any example inputs for this workflow..?

  • Thursday 31 July 2008 13:19:07 (UTC)

    Yes:

    chromosome_name = 17

    start_position = 28500000

    end position = 29500000

  • Monday 25 October 2010 16:23:46 (UTC)
    I like this workflow
  • Thursday 14 April 2011 18:00:32 (UTC)

    I could not run this workflow in Taverna, the error message Faile to oppen workflow name: doesn't appear to be a workflow!

    Other workflows work fine 

    Where do u think the problem?

  • Tuesday 17 May 2011 13:08:51 (UTC)

    Please make sure you have downloaded the workflow and not the workflow image.

  • Friday 08 July 2011 21:17:31 (UTC)

    hi paul my name is eric matute i am from honduras;

     can you help me on how to use taverna  since i'm new around and most do not understand! i'd appreciate it a lot, thanks!!

  • Friday 07 September 2012 18:24:29 (UTC)

    I couldnt execute this workflow :-( Some of the services that are needed are not available

  • Saturday 16 November 2013 05:27:58 (UTC)

    I like this workflow but I could not run this workflow in Taverna.

     




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"This workflow gets a series of information relating to a list of KEGG genes supplied to it. It also removes any null values from a list of strings."This workflow gets a series of information relating to a list of KEGG genes supplied to it. It also removes any null values from a list of strings.

Created: 2011-03-28 | Last updated: 2011-03-28

Credits: User Alibukhari

Workflow Cow-Human Ortholog Pathways and Gene annot... (2)

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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...

Created: 2007-10-03 | Last updated: 2009-12-03