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Pathways and Gene annotations for QTL region (7)

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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...

Created: 2009-11-19 | Last updated: 2012-09-07

Credits: Paul Fisher

Compare genome, extract proteins which are... (1)

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  Takes GI number for source (non-pathogenic) and target (pathogneic) genomes, extracts list of all proteins from each genome using GenBank database. Outputs prtoeins in FastA format. Creates database from source proteins using formatdb (locally installed) and blasts (local installed) proteins from target against this database. Extracts protens which are unique (no blast hits) to the target (pathogenic) genome based on eValue set by user. Takes unique proteins from target and blasts aga...

Created: 2010-03-19 | Last updated: 2010-03-19

Credits: Ian Laycock nclteamc

Attributions: fetchEnsemblSeqsAndBlast NCBI Gi to Kegg Pathways color_pathway_by_objects

NCBI Gi to Kegg Pathways (1)

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User inputs background and foreground colour to be used to highlight proteins in KEGG pathway image. User provides NCBI GI numbers. Worflow calculates KEGG ID and pathway ID and sends value to colour service, which adds colour to that KEGG id on pathway image. Also outputs kegg description, pathway description and url of image.

Created: 2010-03-19 | Last updated: 2010-03-19

Credits: Ian Laycock nclteamc

Attributions: color_pathway_by_objects NCBI Gi to Kegg Pathways

microRNA to KEGG Pathways and Abstracts (1)

Workflow takes in a text file of microRNAs from microCOSM (at the EBI) and outputs a list of KEGG pathway information, including genes in pathways and pathway abstracts from PubMed. The results can then be used in various text mining applications/workflows to rank the results against a given disease.Workflow takes in a file of microRNAs

Created: 2010-03-17

Credits: Paul Fisher

Attributions: Pathways and Gene annotations for QTL region

DataBiNS with Kegg ID (3)

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Consumes a KEGG gene id and mines for pathway, GO, PubMed and SNP information about that gene

Created: 2009-07-09 | Last updated: 2010-11-22

Credits: Mark Wilkinson Fong Chun Chan

Download pathways for external references ... (2)

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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.

Created: 2009-02-03

Credits: Thomaskelder

Get Kegg Pathway information (1)

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This workflow gets a series of information relating to a list of KEGG pathways supplied to it. It also removes any null values from a list of strings. Example input: path:mmu04010 path:mmu05014

Created: 2010-03-10 | Last updated: 2010-03-10

Credits: Paul Fisher

Kegg pathway diagrams (1)

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Find pathways in which all the genes in the list are involved. For each pathway draw the pathway diagram.for each protein draw a diagram of the Kegg pathway that its protein is involved in and where available visualise the structures

Created: 2010-03-13

Credits: Jannetta

Mining the Kegg pathway database with the ... (2)

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Genome-Wide Association studies (GWAS) with metabolomic phenotypes yield several statistically significant SNP-metabolite associations. To understand the biological basis of the association, scientists typically dwell on identifying genes in the vicinity of the SNP and the possible pathways that the gene participates in. The information needed to arrive at an understanding of the mechanistic basis of the association requires integration of disparate data sources. The purpose of this workflow ...

Created: 2012-08-29 | Last updated: 2013-05-15

Credits: Harish Dharuri

UnigeneID to KEGG Pathways (3)

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This workflow accepts a list of Unigene gene identifiers and returns descriptions of gene functions and a list of all pathways each gene is involved in (plus pathway image) from the KEGG database. This workflow replaces the earlier SOAP version with the new KEGG REST services

Created: 2012-01-16 | Last updated: 2012-12-17

Credits: Katy Wolstencroft Paul Fisher

Attributions: NCBI Gi to Kegg Pathways