This workflow uses one or more services that are deprecated as of 31st December 2012 (almost 12 years ago), and may no longer function. Show details...

Pathways and Gene annotations for QTL region

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

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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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Workflow Components

Inputs (3)

Name	Description
chromosome_name
start_position
end_position

Processors (42)

Name	Type	Description
remove_uniprot_duplicates	local
species	stringconstant
kegg_pathway_release	stringconstant
regex_2	stringconstant
split_for_duplicates	local
merge_genes_and_pathways_3	local
merge_genes_and_pathways	local
merge_kegg_references	local
remove_pathway_duplicates	local
merge_pathway_list_1	local
remove_duplicate_ids	local
split_for_duplicate_pathways	local
merge_reports	local
merge_gene_desc	local
remove_duplicate_kegg_genes	local
merge_uniprot_ids	local
remove_entrez_duplicates	local
merge_pathway_list_2	local
merge_pathway_desc	local
merge_entrez_genes	local
merge_genes_and_pathways_2	local
concat_kegg_genes	local
merge_patwhay_ids	local
REMOVE_NULLS_2	beanshell
remove_nulls_3	beanshell
remove_pathway_nulls	beanshell
add_ncbi_to_string	beanshell
remove_Nulls	beanshell
remove_pathway_nulls_2	beanshell
add_uniprot_to_string	beanshell
genes_in_qtl	biomart	Mus musculus genes (NCBIM37)
split_gene_ids	beanshell
mmusculus_gene_ensembl	biomart	Mus musculus genes (NCBIM36)
create_report	beanshell
getcurrentdatabase	soaplabwsdl	Retrieves the current databases from ENSEMBL for a species
flatten_pathway_files	soaplabwsdl	This service flattens a list of KEGG output files to provide a list of KEGG pathways names and their associated gene names
Kegg_gene_ids_2	arbitrarywsdl
binfo	arbitrarywsdl
gene_descriptions	arbitrarywsdl
pathway_descriptions	arbitrarywsdl
Kegg_gene_ids	arbitrarywsdl
Get_pathways	workflow	This workflow removes any null values from a list of strings

Beanshells (11)

Name	Inputs	Outputs
concat_gene_pathway_ids	pathway_ids gene_id	output
concat_ids	input	output
REMOVE_NULLS_2	input	output
remove_nulls_3	input	output
remove_pathway_nulls	input	output
add_ncbi_to_string	input	output
remove_Nulls	input	output
remove_pathway_nulls_2	input	output
add_uniprot_to_string	input	output
split_gene_ids	input	output
create_report	ensemblGene_Id entrezGeneId externalGeneId chromoName geneStart geneEnd ensemblTranscriptId uniprotAcc Affy_Mouse430_2	result

Outputs (9)

Name	Description
merged_pathways
gene_descriptions
pathway_descriptions
ensembl_database_release
kegg_pathway_release
report
kegg_external_gene_reference
pathway_ids
genes_pathways

Links (63)

Source	Sink
Get_pathways:pathway_genes	merge_genes_and_pathways:stringlist
Get_pathways:pathway_ids	merge_pathway_list_1:stringlist
Kegg_gene_ids:return	concat_kegg_genes:string1
Kegg_gene_ids_2:return	concat_kegg_genes:string2
REMOVE_NULLS_2:output	add_uniprot_to_string:input
add_ncbi_to_string:output	Kegg_gene_ids_2:string
add_uniprot_to_string:output	Kegg_gene_ids:string
chromosome_name	genes_in_qtl:mmusculus_gene_ensembl.chromosome_name_filter
concat_kegg_genes:output	merge_kegg_references:stringlist
concat_kegg_genes:output	split_gene_ids:input
create_report:result	merge_reports:stringlist
end_position	genes_in_qtl:mmusculus_gene_ensembl.end_filter
gene_descriptions:return	merge_gene_desc:stringlist
genes_in_qtl:mmusculus_gene_ensembl.ensembl_gene_id	mmusculus_gene_ensembl:mmusculus_gene_ensembl.ensembl_gene_id_filter
kegg_pathway_release:value	binfo:db
merge_entrez_genes:concatenated	remove_Nulls:input
merge_gene_desc:concatenated	remove_nulls_3:input
merge_genes_and_pathways:concatenated	merge_genes_and_pathways_2:stringlist
merge_genes_and_pathways_2:concatenated	merge_genes_and_pathways_3:stringlist
merge_genes_and_pathways_3:concatenated	flatten_pathway_files:merged_pathways_direct_data
merge_pathway_desc:concatenated	remove_pathway_nulls:input
merge_pathway_list_1:concatenated	merge_pathway_list_2:stringlist
merge_pathway_list_2:concatenated	split_for_duplicate_pathways:string
merge_patwhay_ids:concatenated	remove_pathway_nulls_2:input
merge_uniprot_ids:concatenated	REMOVE_NULLS_2:input
mmusculus_gene_ensembl:mmusculus_gene_ensembl.affy_mouse430_2	create_report:Affy_Mouse430_2
mmusculus_gene_ensembl:mmusculus_gene_ensembl.chromosome_name	create_report:chromoName
mmusculus_gene_ensembl:mmusculus_gene_ensembl.end_position	create_report:geneEnd
mmusculus_gene_ensembl:mmusculus_gene_ensembl.ensembl_gene_id	create_report:ensemblGene_Id
mmusculus_gene_ensembl:mmusculus_gene_ensembl.ensembl_transcript_id	create_report:ensemblTranscriptId
mmusculus_gene_ensembl:mmusculus_gene_ensembl.entrezgene	create_report:entrezGeneId
mmusculus_gene_ensembl:mmusculus_gene_ensembl.entrezgene	remove_entrez_duplicates:stringlist
mmusculus_gene_ensembl:mmusculus_gene_ensembl.external_gene_id	create_report:externalGeneId
mmusculus_gene_ensembl:mmusculus_gene_ensembl.start_position	create_report:geneStart
mmusculus_gene_ensembl:mmusculus_gene_ensembl.uniprot_swissprot_accession	remove_uniprot_duplicates:stringlist
pathway_descriptions:return	remove_pathway_duplicates:stringlist
regex_2:value	split_for_duplicate_pathways:regex
regex_2:value	split_for_duplicates:regex
remove_Nulls:output	add_ncbi_to_string:input
remove_duplicate_ids:strippedlist	merge_patwhay_ids:stringlist
remove_duplicate_ids:strippedlist	pathway_descriptions:string
remove_duplicate_kegg_genes:strippedlist	Get_pathways:gene_ids
remove_duplicate_kegg_genes:strippedlist	gene_descriptions:string
remove_entrez_duplicates:strippedlist	merge_entrez_genes:stringlist
remove_nulls_3:output	flatten_pathway_files:gene_descriptions_direct_data
remove_pathway_duplicates:strippedlist	merge_pathway_desc:stringlist
remove_pathway_nulls:output	flatten_pathway_files:pathway_descriptions_direct_data
start_position	genes_in_qtl:mmusculus_gene_ensembl.start_filter
mmusculus_gene_ensembl:mmusculus_gene_ensembl.uniprot_swissprot_accession	create_report:uniprotAcc
remove_uniprot_duplicates:strippedlist	merge_uniprot_ids:stringlist
species:value	getcurrentdatabase:species
split_for_duplicate_pathways:split	remove_duplicate_ids:stringlist
split_for_duplicates:split	remove_duplicate_kegg_genes:stringlist
split_gene_ids:output	split_for_duplicates:string
binfo:return	kegg_pathway_release
flatten_pathway_files:output	genes_pathways
getcurrentdatabase:output	ensembl_database_release
merge_genes_and_pathways_3:concatenated	merged_pathways
merge_kegg_references:concatenated	kegg_external_gene_reference
merge_reports:concatenated	report
remove_nulls_3:output	gene_descriptions
remove_pathway_nulls:output	pathway_descriptions
remove_pathway_nulls_2:output	pathway_ids

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Information Workflow Type

Taverna 1

Information Uploader

Paul Fisher

Information License

All versions of this Workflow are licensed under:

Information Version 5 (of 7)

Information Credits (1)

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Paul Fisher

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Information Statistics

38475 viewings

14148 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:

Pathways and Gene annotations for QTL Phenotype

Created by Paul Fisher on Wednesday 03 October 2007 18:36:02 (UTC)
Pathways and Gene annotations for QTL Phenotype

Created by Paul Fisher on Wednesday 03 October 2007 18:36:02 (UTC)
Mouse QTL Analysis

Created by Paul Fisher on Wednesday 03 October 2007 18:36:02 (UTC)

Last edited by Paul Fisher on Tuesday 28 July 2009 13:06:30 (UTC)

Revision comment:

The older version no longer work due to a change in the KEGG gene mapping web service. This service has been modified to cater for this change.
Pathways and Gene annotations for QTL Phenotype

Created by Paul Fisher on Monday 19 October 2009 18:12:29 (UTC)

Revision comment:

Added a new Soaplab service to combine KEGG pathway and gene names into a single output file.
Pathways and Gene annotations for QTL region

Created by Paul Fisher on Thursday 19 November 2009 18:18:52 (UTC)

Last edited by Paul Fisher on Friday 20 November 2009 10:33:28 (UTC)

Revision comment:

Fixed incorrect workflow outputs and removed duplicates
Pathways and Gene annotations for QTL region - Mouse

Created by Paul Fisher on Tuesday 05 April 2011 10:59:23 (UTC)

Last edited by Paul Fisher on Tuesday 17 May 2011 13:07:55 (UTC)
Pathways and Gene annotations for QTL region

Created by Paul Fisher on Friday 02 September 2011 11:43:00 (UTC)

Last edited by Paul Fisher on Friday 02 September 2011 11:44:57 (UTC)

Revision comment:

Fixed missing lister service

Reviews (1)

Write your own Review

Narenuday

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 (8)

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Stian Soiland-Reyes	Friday 20 June 2008 15:14:48 (UTC)
	Do you have any example inputs for this workflow..?

Paul Fisher

Yes:

chromosome_name = 17

start_position = 28500000

end position = 29500000

Taverna	Monday 25 October 2010 16:23:46 (UTC)
	I like this workflow

Kawther

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?

Paul Fisher	Tuesday 17 May 2011 13:08:51 (UTC)
	Please make sure you have downloaded the workflow and not the workflow image.

Eric Matute

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!!

Khalid Belhajjame	Friday 07 September 2012 18:24:29 (UTC)
	I couldnt execute this workflow :-( Some of the services that are needed are not available

LissaCo...

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

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