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Pathways and Gene annotations for QTL region

Workflow Entry: Pathways and Gene annotations for QTL region

Created at: 19/11/09 @ 18:18:52 Last updated: 02/09/11 @ 11:44:57

Version 7 (latest) (of 7)

Version created on: 02/09/11 @ 11:43:00 by: Paul Fisher | Revision comments 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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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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Workflow Components

Authors (1)

Titles (1)

Descriptions (1)

Inputs (3)

Name	Description
chromosome_name
start_position
end_position

Processors (40)

Name	Type	Description
regex_2	stringconstant
kegg_pathway_release	stringconstant
pathway_descriptions	wsdl	See the Service entry for this web service.
gene_descriptions	wsdl	See the Service entry for this web service.
binfo	wsdl	See the Service entry for this web service.
Kegg_gene_ids	wsdl	See the Service entry for this web service.
flatten_pathway_files	soaplab
Kegg_gene_ids_2	wsdl	See the Service entry for this web service.
remove_nulls_3	beanshell
remove_Nulls	beanshell
REMOVE_NULLS_2	beanshell
split_gene_ids	beanshell
remove_pathway_nulls_2	beanshell
remove_pathway_nulls	beanshell
add_uniprot_to_string	beanshell
add_ncbi_to_string	beanshell
genes_in_qtl	biomart
mmusculus_gene_ensembl	biomart
create_report	beanshell
split_for_duplicates	localworker
merge_reports	localworker
merge_pathway_list_1	localworker
merge_uniprot_ids	localworker
split_for_duplicate_pathways	localworker
remove_entrez_duplicates	localworker
remove_duplicate_ids	localworker
remove_duplicate_kegg_genes	localworker
remove_pathway_duplicates	localworker
merge_pathway_list_2	localworker
merge_kegg_references	localworker
merge_pathway_desc	localworker
merge_entrez_genes	localworker
merge_gene_desc	localworker
merge_genes_and_pathways_2	localworker
merge_genes_and_pathways	localworker
merge_genes_and_pathways_3	localworker
merge_patwhay_ids	localworker
remove_uniprot_duplicates	localworker
concat_kegg_genes	localworker
Get_pathways	workflow

Beanshells (11)

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

Outputs (8)

Name	Description
merged_pathways
gene_descriptions
pathway_descriptions
kegg_pathway_release
report
kegg_external_gene_reference
pathway_ids
genes_pathways

Datalinks (61)

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

Coordinations (0)

Information Workflow Type

Taverna 2

Information Original Uploader

Paul Fisher

Information License

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Information Credits (1)

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Paul Fisher

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Information Featured In Packs (2)

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Information Ratings (8)

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4.9 / 5

(8 ratings)

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Information Attributed By (7)

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Information Favourited By (8)

Information Statistics

10868 viewings

4195 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

Earliest Version:
[1] - Pathways and Gene annotations for QTL Phenotype

Created on: Wednesday 03 October 2007 @ 18:36:02 (GMT)

Created by: Paul Fisher

Revision comments:

None

Previous Versions:
[2] - Pathways and Gene annotations for QTL Phenotype

Created on: Wednesday 03 October 2007 @ 18:36:02 (GMT)

Created by: Paul Fisher

Revision comments:

None

[3] - Mouse QTL Analysis

Created on: Wednesday 03 October 2007 @ 18:36:02 (GMT)

Created by: Paul Fisher

Last edited on: Tuesday 28 July 2009 @ 13:06:30 (GMT)

Last edited by: Paul Fisher

Revision comments:

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.

[4] - Pathways and Gene annotations for QTL Phenotype

Created on: Monday 19 October 2009 @ 18:12:29 (GMT)

Created by: Paul Fisher

Revision comments:

Added a new Soaplab service to combine KEGG pathway and gene names into a single output file.

[5] - Pathways and Gene annotations for QTL region

Created on: Thursday 19 November 2009 @ 18:18:52 (GMT)

Created by: Paul Fisher

Last edited on: Friday 20 November 2009 @ 10:33:28 (GMT)

Last edited by: Paul Fisher

Revision comments:

Fixed incorrect workflow outputs and removed duplicates

[6] - Pathways and Gene annotations for QTL region - Mouse

Created on: Tuesday 05 April 2011 @ 10:59:23 (GMT)

Created by: Paul Fisher

Last edited on: Tuesday 17 May 2011 @ 13:07:55 (GMT)

Last edited by: Paul Fisher

Revision comments:

None

Latest Version:
[7] - Pathways and Gene annotations for QTL region

Created on: Friday 02 September 2011 @ 11:43:00 (GMT)

Created by: Paul Fisher

Last edited on: Friday 02 September 2011 @ 11:44:57 (GMT)

Last edited by: Paul Fisher

Revision comments:

Fixed missing lister service

Reviews (1)

Write your own Review

Narenuday

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 (6)

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Stian Soiland-Reyes	Friday 20 June 2008 @ 15:14:48 (GMT)
	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 (GMT)
	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 (GMT)
	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!!

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Taverna 2

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Bonilla

Pathways and Gene annotations forQTL region (v1)

Created: 20/01/12 @ 09:32:55 | Last updated: 20/01/12 @ 09:32:56

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License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Taverna 2

Original Uploader

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Pathways and Gene annotations for RefSeq ids (v1)

Created: 15/11/10 @ 12:25:01 | Last updated: 15/11/10 @ 12:28:12

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This workflow searches for genes which were found to be differentially expressed from a microarray study in the mouse, Mus musculus. The workflow requires an input of gene ref_seq identifiers. Data is then extracted from BioMart to annotate each of the genes found for each ref_seq id. The Entrez and UniProt identifiers are then sent to KEGG to obtain KEGG gene identifiers. The KEGG gene identifiers are then used to search for pathways in the KEGG pathway database.

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

Viewed: 62 times | Downloaded: 35 times

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