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Showing 23 results. Use the filters on the left and the search box below to refine the results.
Tag: KeggID User: Paul Fisher

Workflow Get Kegg Gene information (2)

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This workflow gets a series of information relating to a list of KEGG genes supplied to it. It also removes any null values from a list of strings.   Example input for this workflow is given below (new line separated): mmu:13163 hsa:1616

Created: 2009-01-26 | Last updated: 2009-12-14

Credits: User Paul Fisher

Workflow Pathways and Gene annotations for QTL region (2)

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This workflow searches for genes which reside in a QTL (Quantitative Trait Loci) region in the Pig, Sus scrofa. 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 pathway ...

Created: 2009-11-20 | Last updated: 2009-11-20

Credits: User Paul Fisher

Attributions: Workflow Pathways and Gene annotations for QTL region

Workflow microRNA to KEGG Pathways and Abstracts (1)

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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: User Paul Fisher

Attributions: Workflow Pathways and Gene annotations for QTL region

Creator

Pack Towards Genotype-Phenotype Correlations


Created: 2009-04-08 13:14:54 | Last updated: 2009-08-11 14:50:01

It is increasingly common to combine Microarray and Quantitative Trait Loci data to aid the search for candidate genes responsible for phenotypic variation. Workflows provide a means of systematically processing large datasets, and represent a framework for the re-use and the explicit declaration of experimental methods. In this pack is a paper which describes the issues facing the manual analysis of microarray and QTL data for the discovery of candidate genes underlying complex phenotypes.&n...

20 items in this pack

Comments: 0 | Viewed: 257 times | Downloaded: 55 times

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Workflow 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: User Paul Fisher

Workflow KEGG Pasrer (1)

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This workflow parses a KEGG species database into an Ondex Graph graphId - the ID of the Graph. inputDir - the plugin input directory Species - Use this parameter to specify the species to be loaded from the kegg database. Default value is all. ParseSequences - KEGG species code. Default value is false (boolean) ImportOrthologFillers - Import Ortholog Pathway Fillers. Default value is false (boolean)

Created: 2009-08-19

Credits: User Paul Fisher

Creator

Pack Genotype to Pathway


Created: 2009-08-11 14:44:16 | Last updated: 2009-08-11 14:52:12

This pack is for investigating links between the genotype of an organisms to possible pathways. This constitutes half of the pathway-driven approach, genotype to pathway, and pathway to phenotype.

18 items in this pack

Comments: 0 | Viewed: 132 times | Downloaded: 19 times

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Blob Kegg pathway identifiers

Created: 2009-04-08 19:28:52 | Last updated: 2009-08-10 11:03:00

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This file contains a list of KEGG pathway identifiers, derived from a list of Ensembl genes found to be located with a given QTL/chromosomal region in the mouse. These genes are located in the Tir1 QTL.

File type: Plain text

Comments: 0 | Viewed: 45 times | Downloaded: 41 times

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Blob Kegg pathway descriptions

Created: 2009-04-08 19:27:55 | Last updated: 2009-08-10 11:29:34

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This file contains a list of KEGG pathway descriptions, identified from genes found within the Tir1 QTL region (for African Trypanosomiasis). Each pathway may contain multiple genes from within the QTL region.

File type: Plain text

Comments: 0 | Viewed: 37 times | Downloaded: 35 times

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Blob Kegg pathways and genes

Created: 2009-04-08 19:26:26 | Last updated: 2009-08-10 11:41:55

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This file contains a list of all genes found within the Tir1 QTL region. These are represented as KEGG gene identifiers. Each gene is listed in tab deliminated format along with all KEGG pathway ids in which the gene is involved. These are given as KEGG pathway identifiers. Each gene may be included in zero or more pathways, with multiple instances of the same pathway being included in the file (due to multiple genes included in a single pathway).

File type: Plain text

Comments: 0 | Viewed: 41 times | Downloaded: 38 times

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