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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

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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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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Workflow Entrez Gene to KEGG Pathway (5)

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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.

Created: 2009-12-04 | Last updated: 2010-11-30

Credits: User Paul Fisher