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KEGG pathways common to both QTL and microarray based investigations

Created: 2009-11-24 17:14:43 Last updated: 2009-12-03 15:28:49

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This workflow takes in two lists of KEGG pathway ids. These are designed to come from pathways found from genes in a QTL (Quantitative Trait Loci) region, and from pathways found from genes differentially expressed in a microarray study. By identifying the intersecting pathways from both studies, a more informative picture is obtained of the candidate processes involved in the expression of a phenotype.

Example input for this workflow is given below (as newline separated values).

qtl_pathways:

path:mmu04060
path:mmu04370
path:mmu04510
path:mmu04060
path:mmu04670
path:mmu00040
path:mmu00150
path:mmu00500
path:mmu00860

microarray_pathways:

path:mmu04060
path:mmu04370
path:mmu00040
path:mmu00150
path:mmu00500
path:mmu00860

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Workflow Components

Inputs (2)

Name	Description
qtl_pathways
microarray_pathways

Processors (6)

Name	Type	Description
kegg_pathways	arbitrarywsdl
common_pathways	soaplabwsdl	Two lists of KEGG pathways are compared and common pathways extracted - for use with QTL and microarray derived pathways
regex	stringconstant
split_pathway_ids	local
merge_pathway_desc	local
remove_null_values	beanshell

Beanshells (1)

Name	Description	Inputs	Outputs
remove_null_values		input	output

Outputs (1)

Name	Description
intersecting_pathways

Links (8)

Source	Sink
microarray_pathways	common_pathways:microarray_pathways_direct_data
qtl_pathways	common_pathways:qtl_pathways_direct_data
common_pathways:output	split_pathway_ids:string
kegg_pathways:return	merge_pathway_desc:stringlist
merge_pathway_desc:concatenated	remove_null_values:input
regex:value	split_pathway_ids:regex
remove_null_values:output	intersecting_pathways
split_pathway_ids:split	kegg_pathways:string

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Taverna 1

Information Uploader

Paul Fisher

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Information Version 3 (latest) (of 3)

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Information Statistics

4953 viewings

3883 downloads

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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

In chronological order:

KEGG pathways common to both QTL and microarray based investigations

Created by Paul Fisher on Wednesday 03 October 2007 18:35:58 (UTC)
KEGG pathways common to both QTL and microarray based investigations

Created by Paul Fisher on Wednesday 03 October 2007 18:35:58 (UTC)

Last edited by Paul Fisher on Tuesday 13 November 2007 16:22:14 (UTC)
KEGG pathways common to both QTL and microarray based investigations

Created by Paul Fisher on Tuesday 24 November 2009 17:14:43 (UTC)

Last edited by Paul Fisher on Thursday 03 December 2009 15:28:50 (UTC)

Revision comment:

Introduced a work around the imposition of a '100 limit' on the number of genes/pathways that can be sent to the KEGG service

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