myExperiment.org - Workflows - Mouse Pathways and Gene annotations for QTL Phenotype (Paul Fisher) [Taverna 1 Workflow]

Workflow Entry: Mouse Pathways and Gene annotations for QTL Phenotype

Created at: 03/10/07 @ 18:36:02 Last updated: 20/02/08 @ 16:05:45

Version 3 (latest) (of 3)

Version created on: 03/10/07 @ 18:36:02 by: Paul Fisher | Revision comments Expand

Last edited on: 20/02/08 @ 16:05:44 by: Paul Fisher

Title: Mouse Pathways and Gene annotations for QTL Phenotype

Type: Taverna 1

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Pathways_and_gene_annotations_for_qtl_phenotype_28303_3

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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

Inputs (3)

Name	Description
chromosome_name
qtl_start_position
qtl_end_position

Processors (37)

Name	Type	Description
kegg_pathway_release	stringconstant
merge_kegg_references	local
merge_pathway_list_1	local
merge_pathway_desc	local
merge_entrez_genes	local
merge_genes_and_pathways	local
merge_uniprot_ids	local
merge_genes_and_pathways_2	local
remove_duplicate_kegg_genes	local
merge_reports	local
merge_genes_and_pathways_3	local
regex_2	stringconstant
species	stringconstant
concat_kegg_genes	local
remove_uniprot_duplicates	local
split_for_duplicates	local
remove_entrez_duplicates	local
merge_pathway_list_2	local
merge_gene_desc	local
genes_in_qtl	biomart	Mus musculus genes (NCBIM36)
mmusculus_gene_ensembl	biomart	Mus musculus genes (NCBIM36)
remove_pathway_nulls	beanshell
REMOVE_NULLS_2	beanshell
add_uniprot_to_string	beanshell
remove_pathway_nulls_2	beanshell
remove_nulls_3	beanshell
add_ncbi_to_string	beanshell
remove_Nulls	beanshell
split_gene_ids	beanshell
create_report	beanshell
getcurrentdatabase	soaplabwsdl	Retrieves the current databases from ENSEMBL for a species
gene_descriptions	arbitrarywsdl
Kegg_gene_ids	arbitrarywsdl
binfo	arbitrarywsdl
Kegg_gene_ids_2	arbitrarywsdl
Get_pathways	workflow	This workflow removes any null values from a list of strings
remove_pathway_duplicates	local

Outputs (8)

Name	Description
merged_pathways
gene_descriptions
pathway_descriptions
ensembl_database_release
kegg_pathway_release
report
kegg_external_gene_reference
pathway_ids

Links (54)

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

Coordinations (0)

Taverna 1 workflow

Information Original Uploader

Paul Fisher

Information License

All versions of this Workflow are licensed under the Creative Commons Attribution-Share Alike 3.0 License.

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Statistics

1431 viewings

1449 downloads

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 (BST)

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 (BST)

Created by: Paul Fisher

Revision comments:

None

Latest Version:
[3] - Mouse Pathways and Gene annotations for QTL Phenotype