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...

Arabidopsis thaliana Microarray Analysis

Created: 2009-07-08 16:28:34

Download Workflow

This workflow searches for genes which are found to be differentially expressed in a microarray study using Arabidopsis thaliana. The workflow requires an input of a list of differentially expressed AffyMetrix Probeset identifiers. Data is then extracted from BioMart to annotate each of the genes. The 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.

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://www.myexperiment.org/workflows/832/download?version=1
[ More Info Expand ]

Workflow Components

Inputs (1)

Name	Description
differentially_expressed_probesets	This port requires a list of differentially expressed probeset identifiers from the affymetrix ATH1 microarray chip

Processors (30)

Name	Type	Description
remove_pathway_duplicates	local
kegg_pathway_release	stringconstant
merge_pathway_list_2	local
merge_kegg_references	local
merge_gene_desc	local
split_for_duplicates	local
merge_uniprot_ids	local
remove_duplicate_kegg_genes	local
merge_genes_and_pathways	local
merge_genes_and_pathways_2	local
merge_genes_and_pathways_3	local
merge_pathway_list_1	local
merge_pathway_desc	local
regex_2	stringconstant
remove_uniprot_duplicates	local
remove_pathway_nulls	beanshell
split_gene_ids	beanshell
add_uniprot_to_string	beanshell
remove_pathway_nulls_2	beanshell
remove_nulls	beanshell
remove_nulls_3	beanshell
Kegg_gene_ids	arbitrarywsdl
gene_descriptions	arbitrarywsdl
binfo	arbitrarywsdl
Get_pathways	workflow	This workflow removes any null values from a list of strings
athaliana_microarray	biomart	Arabidopsis thaliana genes
athaliana_gene_ensembl	biomart	Arabidopsis thaliana genes
merge_pathway_descriptions	local
split_pathway_duplicates	local
remove_duplicate_pathway_ids	local

Beanshells (8)

Name	Inputs	Outputs
concat_ids	input	output
concat_gene_pathway_ids	pathway_ids gene_id	output
remove_pathway_nulls	input	output
split_gene_ids	input	output
add_uniprot_to_string	input	output
remove_pathway_nulls_2	input	output
remove_nulls	input	output
remove_nulls_3	input	output

Outputs (6)

Name	Description
merged_pathways
gene_descriptions
pathway_descriptions
kegg_pathway_release
kegg_external_gene_reference
pathway_ids

Links (36)

Source	Sink
Get_pathways:pathway_desc	merge_pathway_descriptions:stringlist
Get_pathways:pathway_genes	merge_genes_and_pathways:stringlist
Get_pathways:pathway_ids	merge_pathway_list_1:stringlist
Kegg_gene_ids:return	merge_kegg_references:stringlist
Kegg_gene_ids:return	split_gene_ids:input
add_uniprot_to_string:output	Kegg_gene_ids:string
athaliana_gene_ensembl:athaliana_gene_ensembl.uniprot_swissprot	remove_uniprot_duplicates:stringlist
athaliana_microarray:athaliana_gene_ensembl.ensembl_gene_id	athaliana_gene_ensembl:athaliana_gene_ensembl.ensembl_gene_id_filter
differentially_expressed_probesets	athaliana_microarray:athaliana_gene_ensembl.affy_ath1_filter
gene_descriptions:return	merge_gene_desc:stringlist
kegg_pathway_release:value	binfo:db
merge_gene_desc:concatenated	remove_nulls_3:input
merge_genes_and_pathways:concatenated	merge_genes_and_pathways_2:stringlist
merge_genes_and_pathways_2:concatenated	merge_genes_and_pathways_3:stringlist
merge_pathway_desc:concatenated	remove_pathway_nulls:input
merge_pathway_descriptions:concatenated	split_pathway_duplicates:string
merge_pathway_list_1:concatenated	remove_duplicate_pathway_ids:stringlist
regex_2:value	split_pathway_duplicates:regex
remove_duplicate_pathway_ids:strippedlist	merge_pathway_list_2:stringlist
split_pathway_duplicates:split	remove_pathway_duplicates:stringlist
binfo:return	kegg_pathway_release
merge_genes_and_pathways_3:concatenated	merged_pathways
merge_kegg_references:concatenated	kegg_external_gene_reference
merge_pathway_list_2:concatenated	remove_pathway_nulls_2:input
merge_uniprot_ids:concatenated	remove_nulls:input
regex_2:value	split_for_duplicates:regex
remove_duplicate_kegg_genes:strippedlist	Get_pathways:gene_ids
remove_duplicate_kegg_genes:strippedlist	gene_descriptions:string
remove_nulls:output	add_uniprot_to_string:input
remove_nulls_3:output	gene_descriptions
remove_pathway_duplicates:strippedlist	merge_pathway_desc:stringlist
remove_pathway_nulls:output	pathway_descriptions
remove_pathway_nulls_2:output	pathway_ids
remove_uniprot_duplicates:strippedlist	merge_uniprot_ids:stringlist
split_for_duplicates:split	remove_duplicate_kegg_genes:stringlist
split_gene_ids:output	split_for_duplicates:string

Coordinations (0)

Information Workflow Type

Taverna 1

Information Uploader

Paul Fisher

Information License

All versions of this Workflow are licensed under:

Information Version 1 (of 1)

Information Credits (1)

(People/Groups)

Paul Fisher

Information Attributions (0)

(Workflows/Files)

None

Information Tags (19)

Uploader tags

Log in to add Tags

Information Shared with Groups (1)

iPlantCollaborative

Information Featured In Packs (0)

None

Log in to add to one of your Packs

Information Attributed By (0)

(Workflows/Files)

None

Information Favourited By (0)

No one

Information Statistics

2805 viewings

2147 downloads

[ see breakdown ]

Citations (0)

None

Version History

In chronological order:

Arabidopsis thaliana Microarray Analysis

Created by Paul Fisher on Wednesday 08 July 2009 16:28:35 (UTC)

Reviews (0)

No reviews yet

Be the first to review!

Comments (0)

View Timeline

No comments yet

Log in to make a comment

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 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

Taverna 1

Uploader

Paul Fisher

Cow-Human Ortholog Pathways and Gene annot... (2)

Download

This workflow searches for genes which reside in a QTL (Quantitative Trait Loci) region in the cow, Bos taurus. 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. As the Cow genome is currently unfinished, the workflow subsequently maps the cow ensembl gene ids to human orthologues. Entrez and UniProt identifiers are then identified...

Created: 2007-10-03 | Last updated: 2009-12-03