myExperiment - Tags - affymetrix

Workflows (15)

Taverna 1 Original Uploader Pieter Neerincx	AffyArrayQualityAnalysis (v2) Created: 13/03/08 @ 14:38:03 \| Last updated: 16/02/09 @ 16:41:29 Credits: Pieter Neerincx Philipg License: Creative Commons Attribution-Share Alike 3.0 Unported License 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: 177 times \| Downloaded: 56 times Tags (6): affymetrix \| biomoby \| microarray \| nugo \| quality control \| r	View Download (v2)
Taverna 1 Original Uploader Pieter Neerincx	AffyArrayNormalization (v2) Created: 16/02/09 @ 16:32:36 \| Last updated: 16/02/09 @ 16:42:10 Credits: Pieter Neerincx Philipg License: Creative Commons Attribution-Share Alike 3.0 Unported License 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: 208 times \| Downloaded: 85 times Tags (6): affymetrix \| biomoby \| microarray \| normalization \| nugo \| r	View Download (v2)
Taverna 1 Original Uploader Katy Wolstencroft	Gene annotation pipeline for the Graves disease scenario (v2) Created: 03/10/07 @ 18:36:09 \| Last updated: 22/11/07 @ 16:03:15 Credits: Katy Wolstencroft Peter Li License: Creative Commons Attribution-No Derivative Works 3.0 Unported License 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: 562 times \| Downloaded: 195 times Tags (6): affymetirx \| affymetrix \| annotation \| disease \| gene \| graves	View Download (v2)
Taverna 1 Original Uploader Paul Fisher	HUMAN Microarray CEL file to candidate pathways (v4) 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 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: 1216 times \| Downloaded: 359 times Tags (12): affymetrix \| cel \| file \| genotype \| kegg \| microarray \| nbiconworkflows \| pathway-driven \| pathways \| phenotype \| shim	View Download (v4)
Taverna 1 Original Uploader Paul Fisher	Microarray CEL file to candidate pathways (v2) Created: 08/02/08 @ 14:17:23 \| Last updated: 13/02/09 @ 11:29:52 Credits: Paul Fisher Saeedeh License: Creative Commons Attribution-Share Alike 3.0 Unported License 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: 264 times \| Downloaded: 5 times Tags (17): affymetrix \| cel \| data-driven \| ddbj \| disease \| entrez \| gene identifier \| genotype \| kegg \| microarray \| mouse \| pathway \| pathway-driven \| pathways \| shim \| transcribe \| transcription	View
Taverna 1 Original Uploader Paul Fisher	Human Microarray Analysis (v1) Created: 08/02/08 @ 14:30:17 \| Last updated: 03/12/09 @ 16:50:29 Credits: Paul Fisher License: Creative Commons Attribution-Share Alike 3.0 Unported License 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: 268 times \| Downloaded: 4 times Tags (17): affymetrix \| cel \| data-driven \| disease \| expression \| gene \| gene identifier \| genotype \| kegg \| microarray \| pathway \| pathway-driven \| pathways \| shim \| transcribe \| transcription \| uniprot	View
Taverna 2 Original Uploader Francois Belleau	Initialize triplestore with Murin's protocol ontology (v1) Created: 17/02/09 @ 04:40:17 \| Last updated: 17/02/09 @ 04:42:28 Credits: Francois Belleau License: Creative Commons Attribution-Share Alike 3.0 Unported License 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: 40 times \| Downloaded: 23 times Tags (4): affymetrix \| bio2rdf \| murin \| sesame	View Download (v1)
Taverna 2 Original Uploader Francois Belleau	Load affymetrix experiments results into Sesame triplestore for a specific tissue (v1) Created: 17/02/09 @ 04:54:30 Credits: Francois Belleau License: Creative Commons Attribution-Share Alike 3.0 Unported License The affymetrix data source is not public. Rating: 1.0 / 5 (1 rating) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 45 times \| Downloaded: 23 times Tags (4): affymetrix \| bio2rdf \| murin \| sesame	View Download (v1)
Taverna 1 Original Uploader Paul Fisher	Pathways and Gene annotations for Arabidopsis affy data (v2) Created: 06/03/09 @ 17:18:13 \| Last updated: 03/12/09 @ 16:59:11 Credits: Paul Fisher Peter Li Attributions: Pathways and Gene annotations for QTL region License: Creative Commons Attribution-No Derivative Works 3.0 Unported License 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: 216 times \| Downloaded: 1 time Tags (12): affymetrix \| arabidopsis \| binfo \| entrez \| gene \| kegg \| Kegg Pathways \| ncbi \| pathway \| pathways \| swissprot \| uniprot	View
Taverna 1 Original Uploader Paul Fisher	Arabidopsis thaliana Microarray Analysis (v1) Created: 08/07/09 @ 16:28:34 Credits: Paul Fisher License: Creative Commons Attribution-No Derivative Works 3.0 Unported License 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: 142 times \| Downloaded: 28 times Tags (19): affmetrix \| affymetrix \| arabidopsis \| bconv \| data-driven \| ensembl \| gene \| gene expression \| geneid \| genes \| genotype \| kegg \| Kegg Pathways \| microarray \| pathway \| pathways \| phenotype \| thaliana \| uniprot	View Download (v1)
Taverna 2 Original Uploader Paul Fisher	Pathways and Gene annotations for RefSeq ids (v1) Created: 15/11/10 @ 12:25:01 \| Last updated: 15/11/10 @ 12:28:12 Credits: Paul Fisher License: Creative Commons Attribution-Share Alike 3.0 Unported License 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: 62 times \| Downloaded: 35 times Tags (34): affmetrix \| affymetrix \| bconv \| binfo \| chromosome \| common \| data-driven \| database \| disease \| ensembl \| entrez \| expression \| gene \| gene expression \| gene identifier \| geneid \| genes \| genomic \| kegg \| Kegg Pathways \| KeggID \| microarray \| mouse \| pathway \| pathway-driven \| pathways \| phenotype \| species \| swissprot \| trait \| transcribe \| transcription \| trichuris muris \| uniprot	View Download (v1)
Taverna 2 Original Uploader Paul Fisher	KEGG pathways common to both QTL and microarray based investigations (v1) Created: 15/11/10 @ 12:30:21 \| Last updated: 15/11/10 @ 12:30:59 Credits: Paul Fisher License: Creative Commons Attribution-Share Alike 3.0 Unported License 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: 20 times \| Downloaded: 14 times Tags (21): affmetrix \| affymetrix \| binfo \| chromosome \| common \| data-driven \| gene expression \| gene identifier \| geneid \| genotype \| kegg \| Kegg Pathways \| KeggID \| microarray \| pathway \| pathway-driven \| pathways \| phenotype \| qtl \| quanitative \| trait	View Download (v1)
Taverna 2 Original Uploader James Eales	Distance heatmap of GEO dataset produced by RapidAnalytics (v2) Created: 28/04/11 @ 14:15:33 \| Last updated: 13/12/11 @ 16:00:25 Credits: James Eales License: Creative Commons Attribution-Share Alike 3.0 Unported License No description Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 37 times \| Downloaded: 13 times Tags (6): affymetrix \| data mining \| distances \| e-lico \| geo \| heatmap	View Download (v2)
Taverna 2 Original Uploader James Eales	Agglomerative clustering of a GEO dataset using RapidAnalytics (v2) Created: 28/04/11 @ 14:12:33 \| Last updated: 13/12/11 @ 16:00:52 Credits: James Eales License: Creative Commons Attribution-Share Alike 3.0 Unported License No description Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 40 times \| Downloaded: 11 times Tags (5): affymetrix \| clustering \| data mining \| e-lico \| geo	View Download (v2)
Taverna 2 Original Uploader James Eales	Classification of GEO assays using RapidAnalytics (v2) Created: 04/05/11 @ 14:40:17 \| Last updated: 13/12/11 @ 16:01:13 Credits: James Eales License: Creative Commons Attribution-Share Alike 3.0 Unported License No description Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 25 times \| Downloaded: 14 times Tags (9): affymetrix \| assays \| classification \| column \| data mining \| e-lico \| geo \| svm \| table	View Download (v2)

Packs (2)

Creator:

Paul Fisher

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...

20 items in this pack

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Creator:

Paul Fisher

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.

18 items in this pack

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Files (5)

Uploader: Paul Fisher	Candidate Gene protocol Created: 08/04/09 @ 13:27:20 Credits: 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: 33 times \| Downloaded: 38 times Tags: affymetrix \| african trypanosomiasis \| gene \| gene identifier \| geneid \| Kegg Pathways \| KeggID \| pathway \| pathway-driven \| pathways \| phenotype \| sleeping sickness	View Download
Uploader: Paul Fisher	Tir1 QTL - microarray day 7 intersecting pathways Created: 08/04/09 @ 17:57:57 Credits: 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 Rating: 0.0 / 5 (0 ratings) \| Comments: 0 \| Viewed: 21 times \| Downloaded: 23 times Tags: affymetrix \| african trypanosomiasis \| gene \| microarray \| pathway \| qtl \| sleeping sickness	View Download
Uploader: Paul Fisher	Ensembl gene report Created: 08/04/09 @ 19:30:15 \| Last updated: 10/08/09 @ 11:05:59 Credits: 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 Rating: 0.0 / 5 (0 ratings) \| Comments: 0 \| Viewed: 37 times \| Downloaded: 27 times Tags: affymetrix \| base pair \| chromosome \| ensembl \| entrez \| gene \| uniprot	View Download
Uploader: Paul Fisher	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 Rating: 0.0 / 5 (0 ratings) \| Comments: 0 \| Viewed: 5 times \| Downloaded: 4 times Tags: affymetrix \| arrayexpress \| expression \| gene \| gene expression \| madat \| probeset	View Download
Uploader: Paul Fisher	Human Gene expression data - Created: 01/04/11 @ 09:12:28 \| Last updated: 01/04/11 @ 09:12:40 Credits: 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 Rating: 0.0 / 5 (0 ratings) \| Comments: 0 \| Viewed: 6 times \| Downloaded: 5 times Tags: affmetrix \| affymetrix \| gene expression \| gene identifier \| homo sapiens \| human \| kegg \| Kegg Pathways \| madat \| pathway \| pathway-driven \| pathways \| r	View Download

Tag Results

Items tagged with "affymetrix" (22)