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Items tagged with "pathway" (15)

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Pack WikiPathways workflows

Created: 16/09/08 @ 11:43:57 | Last updated: 16/09/08 @ 17:12:35

A set of workflows that use the WikiPathways webservice.

4 items in this pack

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Workflows (14)
Taverna 1

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Workflow Mouse Pathways and Gene annotations for QTL Phenotype (v3)

Created: 03/10/07 @ 18:36:02 | Last updated: 20/02/08 @ 16:05:45

License: Creative Commons Attribution-Share Alike 3.0 License

Pathways_and_gene_annotations_for_qtl_phenotype_28303_3
This workflow searches for genes which reside in a QTL (Quantitative Trait Loci) region in the mouse, Mus musculus. 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 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 path...

Rating: 4.5 / 5 (2 ratings) | Versions: 3 | Reviews: 0 | Comments: 2 | Citations: 1

Viewed: 1436 times | Downloaded: 1455 times

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Taverna 1

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Workflow Entrez Gene to KEGG Pathway (v2)

Created: 03/10/07 @ 18:36:00 | Last updated: 13/11/07 @ 16:16:10

License: Creative Commons Attribution 3.0 License

Entrez_gene_to_kegg_pathway_7493
This workflow takes in Entrez gene ids then adds the string "ncbi-geneid:" to the start of each gene id. These gene ids are then cross-referenced to KEGG gene ids. Each KEGG gene id is then sent to the KEGG pathway database and its relevant pathways returned.

Rating: 4.7 / 5 (3 ratings) | Versions: 2 | Reviews: 0 | Comments: 1 | Citations: 0

Viewed: 1591 times | Downloaded: 985 times

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Taverna 1

Original Uploader

Workflow KEGG pathways common to both QTL and microarray based investigations (v2)

Created: 03/10/07 @ 18:35:58 | Last updated: 13/11/07 @ 16:22:14

License: Creative Commons Attribution-NoDerivs 3.0 License

Kegg_pathways_common_to_both_qtl_and_microarray_based_investigations_27627
This workflow takes in two lists of KEGG pathway ids. These are designed to come from pathways found from genes in a QTL (Quantitative Trait Loci) region, and from pathways found from genes differentially expressed in a microarray study. By identifying the intersecting pathways from both studies, a more informative picture is obtained of the candidate processes involved in the expression of a phenotype

Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 1

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Taverna 1

Original Uploader

Workflow Mapping microarray data onto metabolic pathways (v1)

Created: 14/11/07 @ 16:51:26 | Last updated: 22/11/07 @ 10:39:32

Credits: User Peter Li

License: Creative Commons Attribution-Share Alike 3.0 License

Mapping_microarray_data_onto_metabolic_pathways_3766
This workflow maps microarray data onto metabolic pathway diagrams represented as SBML models drawn using Cell Designer. To run this workflow requires libsbml to be installed into taverna - see http://www.mcisb.org/software/taverna/libsbml/index.html

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 1

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Taverna 1

Original Uploader

Workflow Microarray CEL file to candidate pathways (v2)

Created: 08/02/08 @ 14:17:23 | Last updated: 14/05/08 @ 15:43:23

Credits: User Paul Fisher User Saeedeh

License: Creative Commons Attribution-Share Alike 3.0 License

Microarray_cel_file_to_candidate_pathways_1844_2
This workflow takes in a CEL file and a normalisation method then returns a series of images/graphs which represent the same output obtained using the MADAT software package (MicroArray Data Analysis Tool) [http://www.bioinf.manchester.ac.uk/MADAT/index.html]. Also retruned by this workflow are a list of the top differentialy expressed genes (size dependant on the number specified as input - geneNumber), which are then used to find the candidate pathways which may be influencing the observed ...

Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0

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Taverna 1

Original Uploader

Workflow Human Pathways from Diff Expressed Genes (v1)

Created: 08/02/08 @ 14:30:18 | Last updated: 08/02/08 @ 14:30:19

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 License

Human_pathways_from_diff_expressed_genes_4391_1
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. The final output of the workflow is a list of candidate pathways which are linked to the genes expressed in the microarray data

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 1 | Citations: 0

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Taverna 1

Original Uploader

Workflow Get pathways by external reference (v2)

Created: 16/09/08 @ 11:18:51 | Last updated: 14/11/08 @ 14:21:46

Credits: User Thomaskelder

License: Creative Commons Attribution-Share Alike 3.0 License

Get_pathways_by_external_reference
Finds pathways on WikiPathways by an external gene/protein/metabolite reference. See http://www.pathvisio.org/Help_1.1#Supported_database_systems for a list of supported database systems.

Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0

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Taverna 1

Original Uploader

Workflow Write pathway to disk (v2)

Created: 16/09/08 @ 11:20:54 | Last updated: 14/11/08 @ 14:21:13

Credits: User Thomaskelder

License: Creative Commons Attribution-Share Alike 3.0 License

Write_pathway_to_disk
Downloads and writes a pathway from WikiPathways to a local disk in the given file type.

Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 135 times | Downloaded: 141 times

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Taverna 1

Original Uploader

Workflow Download pathways for external references list (v2)

Created: 16/09/08 @ 11:32:47 | Last updated: 14/11/08 @ 14:38:31

Credits: User Thomaskelder

Attributions: Workflow CloneItemsInList

License: Creative Commons Attribution-Share Alike 3.0 License

Download_pathways_for_external_references_list
Takes a list of external references to genes/proteins/metabolites, finds all pathways on WikiPathways that contain one of the given genes/proteins/metabolites and downloads them in a given file format.

Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 170 times | Downloaded: 123 times

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Taverna 1

Original Uploader

Workflow color_pathway_by_objects (v1)

Created: 01/10/08 @ 17:03:41 | Last updated: 01/10/08 @ 17:06:10

Credits: User Franck Tanoh

License: Creative Commons Attribution-Share Alike 3.0 License

Color_pathway_by_objects_27139_1
Color given objects on a pathway map with specified colors and return the URL of the colored image. In the KEGG pathway maps, a gene or enzyme is represented by a rectangle and a compound is shown as a small circle. Example of input: pathway_id: path:eco00260 object_list: (to add as list) eco:b0514 eco:b2913 fg_color: (to add as list) blue orange bg_color: (to add as list) red orange

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 95 times | Downloaded: 93 times

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Taverna 1

Original Uploader

Workflow get_compounds_by_pathway (v1)

Created: 07/10/08 @ 16:49:19

Credits: User Franck Tanoh

License: Creative Commons Attribution-Share Alike 3.0 License

Get_compounds_by_pathway
Retrieves all compounds on the specified pathway Example of input: path:eco00020

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

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Taverna 1

Original Uploader

Workflow get_drugs_by_pathways (v1)

Created: 07/10/08 @ 17:05:11 | Last updated: 07/10/08 @ 17:05:12

Credits: User Franck Tanoh

License: Creative Commons Attribution-Share Alike 3.0 License

Get_drugs_by_pathways
Retrieves all drugs on the specified pathway. input example: path:map07025 ; path:eco00020

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

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Taverna 1

Original Uploader

Workflow get_element_relations_by_pathway (v1)

Created: 08/10/08 @ 16:19:52

Credits: User Franck Tanoh

License: Creative Commons Attribution-Share Alike 3.0 License

Get_element_relations_by_pathway
Retrieve all objects and relations on specified pathway Input example: path:bsu00010

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

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Taverna 1

Original Uploader

Workflow get_elements_by_pathway (v1)

Created: 08/10/08 @ 16:26:00

Credits: User Franck Tanoh

License: Creative Commons Attribution-Share Alike 3.0 License

Get_elements_by_pathway
Retrieve all objects on specified pathway get_elements_by_pathway Input example: path:bsu00010

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 85 times | Downloaded: 68 times

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