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

Get Pathway-Genes by Entrez gene id

Created: 2012-03-08 11:47:39 Last updated: 2012-04-14 15:14:49

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Given a specific entrez gene id, returns the pathways that this gene participates in and for each of those pathways which genes are associated with.

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Authors (1)

Titles (1)

Descriptions (1)

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Inputs (1)

Name	Description
entrez_gene_id	Give an entrez gene id

Processors (11)

Name	Type	Description
get_pathways_by_genes	wsdl	Wsdl http://soap.genome.jp/KEGG.wsdl Wsdl Operation get_pathways_by_genes
get_genes_by_pathway	wsdl	Wsdl http://soap.genome.jp/KEGG.wsdl Wsdl Operation get_genes_by_pathway
getPathwayDescription	wsdl	Wsdl http://soap.genome.jp/KEGG.wsdl Wsdl Operation btit
add_ncbi_to_string	beanshell	Script String[] split = input.split("\n"); Vector nonEmpty = new Vector(); for (int i = 0; i < split.length; i++) { String trimmed = split[i].trim(); nonEmpty.add(trimmed); } String output = ""; for (int i = 0; i < nonEmpty.size(); i++) { output = output + "ncbi-geneid:" + (String) (nonEmpty.elementAt(i) + "\n"); }
convertToKEGGid	wsdl	Wsdl http://soap.genome.jp/KEGG.wsdl Wsdl Operation bconv
splitAndSendOnlyKEGGgeneID	localworker	Script List split = new ArrayList(); if (!string.equals("")) { String regexString = ","; if (regex != void) { regexString = regex; } String[] result = string.split(regexString); for (int i = 1; i < result.length; i=i+3) { split.add(result[i]); } }
lister	localworker	Script List split = new ArrayList(); if (!string.equals("")) { String regexString = ","; if (regex != void) { regexString = regex; } String[] result = string.split(regexString); for (int i = 0; i < result.length; i++) { split.add(result[i]); } }
splitOnTab	stringconstant	Value \t
SplitOnNewLine	stringconstant	Value \n
Clean_List_of_Strings_by_separator	localworker	Script filteredlist = new ArrayList(); for (Iterator i = stringlist.iterator(); i.hasNext();) { String item = (String) i.next(); String[] tokens = item.split(separators); filteredlist.add(tokens[1]); }
separators_value	stringconstant	Value [:]

Beanshells (1)

Name	Description	Inputs	Outputs
add_ncbi_to_string		input	output

Outputs (2)

Name	Description
Pathway
geneList

Datalinks (13)

Source	Sink
lister:split	get_pathways_by_genes:genes_id_list
get_pathways_by_genes:return	get_genes_by_pathway:pathway_id
get_pathways_by_genes:return	getPathwayDescription:string
entrez_gene_id	add_ncbi_to_string:input
add_ncbi_to_string:output	convertToKEGGid:string
convertToKEGGid:return	splitAndSendOnlyKEGGgeneID:string
splitOnTab:value	splitAndSendOnlyKEGGgeneID:regex
splitAndSendOnlyKEGGgeneID:split	lister:string
SplitOnNewLine:value	lister:regex
get_genes_by_pathway:return	Clean_List_of_Strings_by_separator:stringlist
separators_value:value	Clean_List_of_Strings_by_separator:separators
getPathwayDescription:return	Pathway
Clean_List_of_Strings_by_separator:filteredlist	geneList

Coordinations (0)

Information Workflow Type

Taverna 2

Information Uploader

Eleni

Information License

All versions of this Workflow are licensed under:

Information Version 1 (earliest) (of 4)

Information Credits (1)

(People/Groups)

Eleni

Information Attributions (0)

(Workflows/Files)

None

Information Tags (6)

Uploader tags

entrez
|
gene
|
id
|
kegg
|
pathway
|
pathways

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Information Attributed By (0)

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Information Favourited By (0)

No one

Information Statistics

2881 viewings

1530 downloads

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Citations (0)

None

Version History

In chronological order:

Get Pathway-Genes by Entrez gene id

Created by Eleni on Thursday 08 March 2012 11:47:39 (UTC)
Get Pathway-Genes by Entrez gene id

Created by Eleni on Tuesday 27 March 2012 12:38:25 (UTC)

Revision comment:

possibly a space at the details section was causing an error when was run as a galaxy tool, on galaxy
Get Pathway-Genes by Entrez gene id

Created by Eleni on Saturday 14 April 2012 15:01:10 (UTC)

Revision comment:

Added extra output with the KEGG pathway map
Get Pathway-Genes by Entrez gene id

Created by Eleni on Saturday 14 April 2012 15:14:49 (UTC)

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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...

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Get Pathway-Genes by Entrez gene id

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