Workflows

Arabidopsis thaliana QTL Analysis (1)

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This workflow searches for genes which reside in a QTL (Quantitative Trait Loci) region in Arabidopsis thaliana. 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 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. ...

Created: 2009-07-08 | Last updated: 2009-12-14

Credits: Paul Fisher

get_enzymes_by_gene (1)

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Retrieve all the EC numbers which are assigned to a given gene Input example: eco:b0002

Created: 2008-10-08

Credits: Franck Tanoh

bconv (1)

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Converts external IDs to KEGG IDs.External database:  NCBI GI, NCBI GeneID, GenBank , UniGene , OMIM. Database prefix: ncbi-gi:, ncbi-geneid:, genbank: ,unigene: , uniprot: , omim: Example of input parameter: ncbi-gi:10047090 ncbi-geneid:14751

Created: 2008-09-29 | Last updated: 2008-09-29

Credits: Franck Tanoh

Microarray CEL file to candidate pathways (2)

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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 ...

Created: 2007-10-03

Retrieve Pathways and Compound information... (1)

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Given a KEGG compound identifier (e.g. cpd:C00905), this workflow queries KEGG DB for pathways and compound information for each of these compounds. As the KEGG pathway service tries to find pathways which contain all input compounds, the input list is split up to circumvent this behaviour and to search for only one compound in a pathway at a time. Compounds identified in pathways are marked as red in the resulting pathway image.

Created: 2009-03-30 | Last updated: 2009-03-30

Credits: Michael Gerlich

Kegg_DrugID (1)

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 This workflow accepts looks up drug identifiers from KEGG given a pathway identifier. You can enter a pathway ID in the form path:map07026

Created: 2009-03-18 | Last updated: 2009-03-18

Credits: Rory

get_elements_by_pathway (1)

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

Created: 2008-10-08

Credits: Franck Tanoh

get_element_relations_by_pathway (1)

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

Created: 2008-10-08

Credits: Franck Tanoh

get_drugs_by_pathways (1)

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

Created: 2008-10-07

Credits: Franck Tanoh

color_pathway_by_elements (2)

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Color the objects (rectangles and circles on a pathway map) corresponding to the given 'element_id_list' with the specified colors and return the URL of the colored image. Example of inputs: pathway_id: path:bsu00010 element_list: (to add as list) 78 79 fg_color_list:(to add as list) red blue bg_color_list: (to add as list) green yellow

Created: 2008-09-30 | Last updated: 2008-10-01

Credits: Franck Tanoh