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

Mouse Microarray Analysis

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

Download Workflow

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.

Preview

Download as scalable diagram (SVG)

Run

Run this Workflow in the Taverna Workbench...

Option 1:

Copy and paste this link into File > 'Open workflow location...'
http://myexperiment.org/workflows/19/download?version=1
[ More Info Expand ]

Workflow Components

Inputs (1)

Name	Description
probeset_list

Processors (35)

Name	Type	Description
concat_kegg_genes	local
split_probesets	local
split_for_duplicates	local
merge_pathway_ids_2	local
merge_gene_desc	local
merge_genes_and_pathways	local
regex_2	stringconstant
merge_entrez_genes	local
merge_genes_pathways_3	local
remove_duplicate_kegg_genes	local
species	stringconstant
remove_pathway_duplicates	local
kegg_pathway_release	stringconstant
remove_uniprot_duplicates	local
remove_entrez_duplicates	local
merge_pathway_desc	local
merge_genes_pathways_2	local
merge_pathway_ids_1	local
merge_reports	local
merge_uniprot_ids	local
add_ncbi_to_string	beanshell
REMOVE_NULLS_2	beanshell
add_uniprot_to_string	beanshell
remove_description_nulls	beanshell
Kegg_gene_ids_2	arbitrarywsdl
remove_pathway_nulls	beanshell
split_gene_ids	beanshell
gene_descriptions	arbitrarywsdl
remove_Nulls	beanshell
create_report	beanshell
mmusculus_gene_ensembl	biomart	Mus musculus genes (NCBIM36)
Kegg_gene_ids	arbitrarywsdl
binfo	arbitrarywsdl
Get_Pathways	workflow	This workflow removes any null values from a list of strings
getcurrentdatabase	soaplabwsdl	Retrieves the current databases from ENSEMBL for a species

Beanshells (10)

Name	Inputs	Outputs
concat_ids	input	output
concat_gene_pathway_ids	pathway_ids gene_id	output
add_ncbi_to_string	input	output
REMOVE_NULLS_2	input	output
add_uniprot_to_string	input	output
remove_description_nulls	input	output
remove_pathway_nulls	input	output
split_gene_ids	input	output
remove_Nulls	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
report
pathway_list

Links (49)

Source	Sink
Get_Pathways:pathway_desc	merge_pathway_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_gene_ids:input
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
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.uniprot_swissprot_accession	create_report:uniprotAcc
mmusculus_gene_ensembl:mmusculus_gene_ensembl.uniprot_swissprot_accession	remove_uniprot_duplicates:stringlist
probeset_list	split_probesets:string
regex_2:value	split_for_duplicates:regex
regex_2:value	split_probesets:regex
remove_Nulls:output	add_ncbi_to_string:input
remove_duplicate_kegg_genes:strippedlist	Get_Pathways:gene_ids
remove_duplicate_kegg_genes:strippedlist	gene_descriptions:string
split_gene_ids:output	split_for_duplicates:string
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
mmusculus_gene_ensembl:mmusculus_gene_ensembl.external_gene_id	create_report:externalGeneId
mmusculus_gene_ensembl:mmusculus_gene_ensembl.start_position	create_report:geneStart
remove_description_nulls:output	gene_descriptions
remove_entrez_duplicates:strippedlist	merge_entrez_genes:stringlist
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_probesets:split	mmusculus_gene_ensembl:mmusculus_gene_ensembl.affy_mouse430_2_filter

Coordinations (0)

Information Workflow Type

Taverna 1

Information Uploader

Paul Fisher

Information License

All versions of this Workflow are licensed under:

Information Version 1 (earliest) (of 3)

Information Credits (0)

(People/Groups)

None

Information Attributions (0)

(Workflows/Files)

None

Information Tags (17)

Uploader tags

Log in to add Tags

Information Shared with Groups (0)

None

Information Featured In Packs (3)

Log in to add to one of your Packs

Information Attributed By (0)

(Workflows/Files)

None

Information Favourited By (0)

No one

Information Statistics

5955 viewings

4275 downloads

[ see breakdown ]

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.

Reviews (0)

No reviews yet

Be the first to review!

Comments (1)

View Timeline

Log in to make a comment

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

Other workflows that use similar services (98)

Only the first 2 workflows that use similar services are shown. View all workflows that use these services.

Taverna 1

Uploader

Antoon Goderis

qtl_pathway_3.xml (1)

Download

No description

Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

Taverna 2

Uploader

Paul Fisher

Pathways and Gene annotations for QTL region (1)

Download

This workflow searches for genes which reside in a QTL (Quantitative Trait Loci) region in rice, Oryza sativa. 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 UniGene 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 d...

Created: 2011-05-27 | Last updated: 2011-05-27

Credits: Paul Fisher