myExperiment.org - Workflows - Pathways from Diff Expressed Genes (Paul Fisher) [Taverna 1 Workflow]

Workflow Entry: Pathways from Diff Expressed Genes

Created at: 03/10/07 @ 18:36:05 Last updated: 11/07/08 @ 10:52:01

Version 3 (latest) (of 3)

Version created on: 03/10/07 @ 18:36:05 by: Paul Fisher | Revision comments Expand

Last edited on: 11/07/08 @ 10:52:01 by: Paul Fisher

Title: Pathways from Diff Expressed Genes

Type: Taverna 1

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Description

This workflow takes in probesets from and AffyMetrix micorarray experiment and returns: the genes in the QTL; gene start and end positions; chromosome where genes reside; ensembl trasncripts; SwissProt ids; affy probeset identifiers for chips Mouse430_2 and Mouse430a_2.

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http://www.myexperiment.org/workflows/19/download?version=3
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Workflow Components

Inputs (1)

Name	Description
probeset_list

Processors (36)

Name	Type	Description
species	stringconstant
remove_duplicate_kegg_genes	local
merge_pathway_desc	local
merge_gene_desc	local
concat_kegg_genes	local
split_probesets	local
remove_duplicate_desc	local
merge_genes_and_pathways	local
merge_pathway_ids_1	local
merge_genes_pathways_2	local
remove_uniprot_duplicates	local
kegg_pathway_release	stringconstant
split_for_duplicates	local
regex_2	stringconstant
merge_uniprot_ids	local
merge_entrez_genes	local
merge_reports	local
remove_pathway_duplicates	local
merge_pathway_ids_2	local
remove_entrez_duplicates	local
merge_genes_pathways_3	local
add_uniprot_to_string	beanshell
remove_description_nulls	beanshell
REMOVE_NULLS_2	beanshell
remove_Nulls	beanshell
split_gene_ids	beanshell
remove_pathway_nulls	beanshell
add_ncbi_to_string	beanshell
create_report	beanshell
getcurrentdatabase	soaplabwsdl	Retrieves the current databases from ENSEMBL for a species
Kegg_gene_ids_2	arbitrarywsdl
Kegg_gene_ids	arbitrarywsdl
gene_descriptions	arbitrarywsdl
binfo	arbitrarywsdl
Get_Pathways	workflow	This workflow removes any null values from a list of strings
mmusculus_gene_ensembl	biomart	Mus musculus genes (NCBIM37)

Outputs (7)

Name	Description
merged_pathways
gene_descriptions
pathway_descriptions
ensembl_database_release
kegg_pathway_release
pathway_list
report

Links (50)

Sink	Source
remove_duplicate_desc:stringlist	Get_Pathways:pathway_desc
merge_genes_and_pathways:stringlist	Get_Pathways:pathway_genes
merge_pathway_ids_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
split_for_duplicates:string	concat_kegg_genes:output
merge_reports:stringlist	create_report:result
merge_gene_desc:stringlist	gene_descriptions:return
binfo:db	kegg_pathway_release:value
remove_Nulls:input	merge_entrez_genes:concatenated
remove_description_nulls:input	merge_gene_desc:concatenated
merge_genes_pathways_2:stringlist	merge_genes_and_pathways:concatenated
merge_genes_pathways_3:stringlist	merge_genes_pathways_2:concatenated
remove_pathway_nulls:input	merge_pathway_desc:concatenated
remove_pathway_duplicates:stringlist	merge_pathway_ids_1:concatenated
REMOVE_NULLS_2:input	merge_uniprot_ids:concatenated
split_probesets:string	probeset_list
create_report:chromoName	mmusculus_gene_ensembl:mmusculus_gene_ensembl.chromosome_name
create_report:geneEnd	mmusculus_gene_ensembl:mmusculus_gene_ensembl.end_position
create_report:ensemblGeneId	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
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
split_probesets:regex	regex_2:value
add_ncbi_to_string:input	remove_Nulls:output
merge_pathway_desc:stringlist	remove_duplicate_desc:strippedlist
split_gene_ids:input	remove_duplicate_kegg_genes:strippedlist
merge_entrez_genes:stringlist	remove_entrez_duplicates:strippedlist
mmusculus_gene_ensembl:mmusculus_gene_ensembl.affy_mouse430a_2_filter	split_probesets:split
kegg_pathway_release	binfo:return
ensembl_database_release	getcurrentdatabase:output
merged_pathways	merge_genes_pathways_3:concatenated
pathway_list	merge_pathway_ids_2:concatenated
report	merge_reports:concatenated
gene_descriptions	remove_description_nulls:output
merge_pathway_ids_2:stringlist	remove_pathway_duplicates:strippedlist
pathway_descriptions	remove_pathway_nulls:output
merge_uniprot_ids:stringlist	remove_uniprot_duplicates:strippedlist
getcurrentdatabase:species	species:value
remove_duplicate_kegg_genes:stringlist	split_for_duplicates:split
Get_Pathways:gene_ids	split_gene_ids:output
gene_descriptions:string	split_gene_ids: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

1154 viewings

1072 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 from Diff Expressed Genes

Created on: Wednesday 03 October 2007 @ 18:36:05 (BST)

Created by: Paul Fisher

Revision comments:

None

Previous Versions:
[2] - MOUSE Pathways from Diff Expressed Genes

Created on: Wednesday 03 October 2007 @ 18:36:05 (BST)

Created by: Paul Fisher

Last edited on: Wednesday 20 February 2008 @ 16:01:39 (GMT)

Last edited by: Paul Fisher

Revision comments: