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Mouse Microarray Analysis

Created: 2007-10-03 18:36:05 Last updated: 2009-12-03 16:20:33

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

Example ids from the Mouse430_2 affymetrix array are as follows (newline separated):

1447227_at
1440624_at
1436240_at
1454904_at
1435665_at
1418148_at
1429831_at

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http://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)

Beanshells (10)

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

Outputs (7)

Name	Description
merged_pathways
gene_descriptions
pathway_descriptions
ensembl_database_release
kegg_pathway_release
pathway_list
report

Links (50)

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

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Taverna 1

Information Uploader

Paul Fisher

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Information Statistics

5898 viewings

4233 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 from Diff Expressed Genes

Created by Paul Fisher on Wednesday 03 October 2007 18:36:05 (UTC)
MOUSE Pathways from Diff Expressed Genes

Created by Paul Fisher on Wednesday 03 October 2007 18:36:05 (UTC)

Last edited by Paul Fisher on Wednesday 20 February 2008 16:01:39 (UTC)
Mouse Microarray Analysis

Created by Paul Fisher on Wednesday 03 October 2007 18:36:05 (UTC)

Last edited by Paul Fisher on Thursday 03 December 2009 16:20:34 (UTC)

Revision comment:

Change to the BioMart processor.

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Stian Soiland-Reyes	Friday 20 June 2008 15:15:40 (UTC)
	Do you have some example inputs for running this workflow..?

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