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Items tagged with "affymetrix" (22)

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Files (5)
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Blob Candidate Gene protocol

Created: 08/04/09 @ 13:27:20

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This protocol provides details on how to identify candidate genes from the returned workflow results.

File type: Word document

Rating: 0.0 / 5 (0 ratings) | Comments: 0 | Viewed: 41 times | Downloaded: 43 times

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Blob Tir1 QTL - microarray day 7 intersecting pathways

Created: 08/04/09 @ 17:57:57

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This spreadhseet contains all of the intersecting pathways between the Tir1 QTL and day 7 differentially expressed genes

File type: Excel workbook

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Blob Ensembl gene report

Created: 08/04/09 @ 19:30:15 | Last updated: 10/08/09 @ 11:05:59

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This file contains all genes identified in the Tir1 QTL region. Each gene is (if available) associated with an Entrez, UniProt, External Gene Id, Affymetrix probeset identifers (mouse_430_A chip), and Ensembl identifers for genes and their transcripts.

File type: Plain text

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Blob Human Probeset data from Affymetrix

Created: 01/04/11 @ 09:08:45 | Last updated: 01/04/11 @ 09:08:51

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This file contains a list or affymetrix probest identifiers for Human gene expression data relating to the: Impact of NRSF variant over-expression in SK-N-AS human neuroblastoma cells (http://www.ebi.ac.uk/arrayexpress/browse.html?keywords=E-GEOD-22467&expandefo=on)

File type: Plain text

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Blob Human Gene expression data -

Created: 01/04/11 @ 09:12:28 | Last updated: 01/04/11 @ 09:12:40

Credits: User Saeedeh

Attributions:

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This file contains a list processed  for Human gene expression CEL files relating to the: Impact of NRSF variant over-expression in SK-N-AS human neuroblastoma cells (http://www.ebi.ac.uk/arrayexpress/browse.html?keywords=E-GEOD-22467&expandefo=on). The CEL files were analysed using the MADAT Taverna workflow available on myExperiment: http://www.myexperiment.org/workflows/2002.html

File type: ZIP archive

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Workflows (15)
Original Uploader

Workflow AffyArrayQualityAnalysis (2)

Created: 13/03/08 @ 14:38:03 | Last updated: 16/02/09 @ 16:41:29

Credits: User Pieter Neerincx User Philipg

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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...

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

Viewed: 206 times | Downloaded: 63 times

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Original Uploader

Workflow AffyArrayNormalization (2)

Created: 16/02/09 @ 16:32:36 | Last updated: 16/02/09 @ 16:42:10

Credits: User Pieter Neerincx User Philipg

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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 ...

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

Viewed: 226 times | Downloaded: 107 times

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Original Uploader

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

Created: 03/10/07 @ 18:36:09 | Last updated: 22/11/07 @ 16:03:15

Credits: User Katy Wolstencroft User Peter Li

License: Creative Commons Attribution-No Derivative Works 3.0 Unported License

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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.

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

Viewed: 664 times | Downloaded: 218 times

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Original Uploader

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

Created: 03/10/07 @ 18:35:55 | Last updated: 26/11/09 @ 17:34:24

License: Creative Commons Attribution-No Derivative Works 3.0 Unported License

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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 ...

Rating: 5.0 / 5 (2 ratings) | Versions: 4 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 1463 times | Downloaded: 413 times

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Original Uploader

Workflow Microarray CEL file to candidate pathways (2)

Created: 08/02/08 @ 14:17:23 | Last updated: 13/02/09 @ 11:29:52

Credits: User Paul Fisher User Saeedeh

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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 ch...

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

Viewed: 296 times | Downloaded: 5 times

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Original Uploader

Workflow Human Microarray Analysis (1)

Created: 08/02/08 @ 14:30:17 | Last updated: 03/12/09 @ 16:50:29

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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  

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

Viewed: 293 times | Downloaded: 4 times

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Original Uploader

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

Created: 17/02/09 @ 04:40:17 | Last updated: 17/02/09 @ 04:42:28

Credits: User Francois Belleau

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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.

Rating: 1.0 / 5 (1 rating) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 45 times | Downloaded: 27 times

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Original Uploader

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

Created: 06/03/09 @ 17:18:13 | Last updated: 03/12/09 @ 16:59:11

Credits: User Paul Fisher User Peter Li

Attributions: Workflow Pathways and Gene annotations for QTL region

License: Creative Commons Attribution-No Derivative Works 3.0 Unported License

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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.

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

Viewed: 237 times | Downloaded: 1 time

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Original Uploader

Workflow Arabidopsis thaliana Microarray Analysis (1)

Created: 08/07/09 @ 16:28:34

Credits: User Paul Fisher

License: Creative Commons Attribution-No Derivative Works 3.0 Unported License

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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.

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

Viewed: 163 times | Downloaded: 35 times

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Original Uploader

Workflow Pathways and Gene annotations for RefSeq ids (1)

Created: 15/11/10 @ 12:25:01 | Last updated: 15/11/10 @ 12:28:12

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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.

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

Viewed: 85 times | Downloaded: 36 times

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Original Uploader

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

Created: 15/11/10 @ 12:30:21 | Last updated: 15/11/10 @ 12:30:59

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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

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

Viewed: 35 times | Downloaded: 17 times

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Original Uploader

Workflow Distance heatmap of GEO dataset produced b... (2)

Created: 28/04/11 @ 14:15:33 | Last updated: 13/12/11 @ 16:00:25

Credits: User James Eales

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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

Viewed: 48 times | Downloaded: 24 times

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Original Uploader

Workflow Agglomerative clustering of a GEO dataset ... (2)

Created: 28/04/11 @ 14:12:33 | Last updated: 13/12/11 @ 16:00:52

Credits: User James Eales

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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

Viewed: 63 times | Downloaded: 27 times

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Packs (2)
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Pack Towards Genotype-Phenotype Correlations


Created: 08/04/09 @ 13:14:54 | Last updated: 11/08/09 @ 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...

1 item in this pack

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Pack Genotype to Pathway


Created: 11/08/09 @ 14:44:16 | Last updated: 11/08/09 @ 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.

0 items in this pack

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Non-Information Resource URI: http://alpha.myexperiment.org/tags/748


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