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Workflow Entry: Pathways and Gene annotations for QTL region

Created at: 19/11/09 @ 18:18:52      Last updated: 07/09/12 @ 18:23:36
Information Version 7 (latest) (of 7)
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Version created on: 02/09/11 @ 11:43:00 by: Paul Fisher   |   Revision comment Expand

Last edited on: 02/09/11 @ 11:44:57 by: Paul Fisher

Title: Pathways and Gene annotations for QTL region

Type: Taverna 2


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Information Description

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.


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http://www.myexperiment.org/workflows/16/download?version=7
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Information Workflow Components

Information Authors (1)
Information Titles (1)
Information Descriptions (1)
Information Dependencies (0)
Inputs (3)
Processors (40)
Beanshells (11)
Outputs (8)
Datalinks (61)
Coordinations (0)

Information Workflow Type

Taverna 2

Information Original Uploader

Information License

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Information Credits (1)

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Information Tags (21)

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Information Featured In Packs (4)

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Information Ratings (10)

Current:

4.6 / 5

(10 ratings)

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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


Version History

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Reviews Reviews (1)

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Review Title: asdlfkj

Rating: 5 out of 5

Created: 01/12/11 @ 07:21:30 | Updated: 01/12/11 @ 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.

     




Workflow Other workflows that use similar services (93)

Only the first 2 workflows that use similar services are shown. View all workflows that use these services.


Original Uploader

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

Created: 03/10/07 @ 18:36:00 | Last updated: 03/12/09 @ 16:16:31

License: Creative Commons Attribution-No Derivative Works 3.0 Unported License

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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...

Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 1 | Citations: 0

Viewed: 329 times | Downloaded: 77 times

Tags (1):

Original Uploader

Workflow Entrez Gene to KEGG Pathway (5)

Created: 04/12/09 @ 16:04:38 | Last updated: 30/11/10 @ 12:18:53

Credits: User Paul Fisher

License: Creative Commons Attribution 3.0 Unported License

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This workflow takes in Entrez gene ids then adds the string "ncbi-geneid:" to the start of each gene id. These gene ids are then cross-referenced to KEGG gene ids. Each KEGG gene id is then sent to the KEGG pathway database and its relevant pathways returned.

Rating: 4.8 / 5 (4 ratings) | Versions: 5 | Reviews: 0 | Comments: 3 | Citations: 0

Viewed: 1649 times | Downloaded: 630 times

Tags (9):

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Linked Data

Non-Information Resource URI: http://www.myexperiment.org/workflows/16


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