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Candidate Gene protocol

Created: 2009-04-08 13:27:20

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: Word document

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Tir1 QTL - microarray day 7 intersecting pathways

Created: 2009-04-08 17:57:57

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: Excel workbook

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Ensembl gene report

Created: 2009-04-08 19:30:15 | Last updated: 2009-08-10 11:05:59

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: Plain text

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Human Probeset data from Affymetrix

Created: 2011-04-01 09:08:45 | Last updated: 2011-04-01 09:08:51

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: Plain text

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Human Gene expression data -

Created: 2011-04-01 09:12:28 | Last updated: 2011-04-01 09:12:40

Credits: Saeedeh

Attributions:

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: ZIP archive

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Towards Genotype-Phenotype Correlations

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

20 items in this pack

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Genotype to Pathway

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

18 items in this pack

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AffyArrayQualityAnalysis (2)

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The AffyArrayQualityAnalysis web services provide quality control for raw Affymetrix GeneChip data. They are wrappers around Philip de Groot's quality control R script to provide remote programmatic access. This example workflow demonstrates the use of the AffyArrayQualityAnalysis services. The flow is as follows: A client executes the AffyArrayQualityAnalysis_submit service with two inputs: a User object and a collection of URLs linking to CEL files. The User object contains a u...

Created: 2008-03-13 | Last updated: 2009-02-16

Credits: Pieter Neerincx Philipg

AffyArrayNormalization (2)

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The AffyArrayNormalization web services normalise raw Affymetrix GeneChip data. They are wrappers around Philip de Groot's normalization R script to provide remote programmatic access. This example workflow demonstrates the use of the AffyArrayNormalization services. The flow is as follows: A client executes the AffyArrayNormalization_submit service with two inputs: a User object and a collection of URLs linking to CEL files. The User object contains a user ID, a password and an ...

Created: 2009-02-16 | Last updated: 2009-02-16

Credits: Pieter Neerincx Philipg

Gene annotation pipeline for the Graves di... (2)

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This is a revised workflow for the Graves disease scenario gene annotation pipeline used in the myGrid project. The workflow had to be re-written due to the loss of the services invoked in the original workflow.

Created: 2007-10-03 | Last updated: 2007-11-22

Credits: Katy Wolstencroft Peter Li

HUMAN Microarray CEL file to candidate pat... (4)

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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 returned 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 | Last updated: 2009-11-26

Microarray CEL file to candidate pathways (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 ch...

Created: 2008-02-08 | Last updated: 2009-02-13

Credits: Paul Fisher Saeedeh

Human Microarray Analysis (1)

This workflow takes in probesets from and AffyMetrix  Affy HG U133A micorarray experiment and returns: genes ; gene start and end positions; chromosome where genes reside; ensembl trasncripts; SwissProt ids. The final output of the workflow is a list of candidate pathways which are linked to the genes expressed in the microarray data.   Example input for this workflow is: 212283_at 221634_at 220399_at  

Created: 2008-02-08 | Last updated: 2009-12-03

Credits: Paul Fisher

Initialize triplestore with Murin's protoc... (1)

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This workflow initialize the Sesame triplestore with initial data.  The 5 rdfiser in JSP are needed, they are executed on localhost.

Created: 2009-02-17 | Last updated: 2009-02-17

Credits: Francois Belleau

Load affymetrix experiments results into S... (1)

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The affymetrix data source is not public.

Created: 2009-02-17

Credits: Francois Belleau

Pathways and Gene annotations for Arabidop... (2)

This workflow searches for genes obtained from affy_ath1 affymetrix probeset identifiers. 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 database.

Created: 2009-03-06 | Last updated: 2009-12-03

Credits: Paul Fisher Peter Li

Attributions: Pathways and Gene annotations for QTL region

Arabidopsis thaliana Microarray Analysis (1)

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This workflow searches for genes which are found to be differentially expressed in a microarray study using Arabidopsis thaliana. The workflow requires an input of a list of differentially expressed AffyMetrix Probeset identifiers. Data is then extracted from BioMart to annotate each of the genes. 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

Credits: Paul Fisher

Pathways and Gene annotations for RefSeq ids (1)

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This workflow searches for genes which were found to be differentially expressed from a microarray study in the mouse, Mus musculus. The workflow requires an input of gene ref_seq identifiers. Data is then extracted from BioMart to annotate each of the genes found for each ref_seq id. The Entrez and UniProt identifiers are then sent to KEGG to obtain KEGG gene identifiers. The KEGG gene identifiers are then used to search for pathways in the KEGG pathway database.

Created: 2010-11-15 | Last updated: 2010-11-15

Credits: Paul Fisher

KEGG pathways common to both QTL and micro... (1)

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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

Created: 2010-11-15 | Last updated: 2010-11-15

Credits: Paul Fisher

Gene set enrichment analysis (Affymetrix p... (1)

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This workflow is designed to perform Gene Set Enrichment Analysis, GSEA, as it is described at http://www.broadinstitute.org/gsea/index.jsp. As input, the normalized data with Affymetrix probeset IDs can be submitted.First, the input files are subjected to fold-change calculation. The table with probeset Ids and calculated fold change values is converted into a table with Ensembl Gene Ids. At the next step, the Ensembl genes are annotated with additional information, gene description and gene...

Created: 2013-10-29 | Last updated: 2015-04-17

Credits: geneXplain

Download data from array express + create ... (1)

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This workflow uses the array express library to download data from the array express repository and creates two separate files. The gene expression and the phenotype files. The files are saved in the directory that the user has to specify in the input. NOTE: The library(ArrayExpress) is a prerequisite for this workflow

Created: 2013-11-04

Credits: Eleni