myExperiment - Tags - microarray

Packs (4)

Creator: Peter Li	Microarray data analysis using R Created: 02/07/08 @ 11:30:06 No description 3 items in this pack Comments: 0 \| Viewed: 173 times \| Downloaded: 36 times Tags: bioconductor \| limma \| maxd \| microarray \| r	View Download
Creator: Katy Wolstencroft	useful_for_sysmo Created: 17/12/08 @ 12:31:48 \| Last updated: 08/03/09 @ 12:52:47 These workflows have been collected as potentially useful protocols for the sysmo consortium 21 items in this pack Comments: 0 \| Viewed: 104 times \| Downloaded: 15 times Tags: cdk-taverna \| cheminformatics \| chemoinformatics \| microarray \| pathway \| systems biology	View Download
Creator: Wassinki	Package: mapping oligonucleotides to an assembly Created: 11/12/08 @ 12:02:47 \| Last updated: 22/01/09 @ 09:06:26 This package contains all elements required to run the RShell use case "Mapping oligonucleotides to an assembly" 5 items in this pack Comments: 0 \| Viewed: 119 times \| Downloaded: 41 times Tags: biomart \| BLAST \| blat \| danio_rerio_genome \| ensembl \| microarray \| r \| rshell \| vega	View Download
Creator: Paul Fisher	Towards Genotype-Phenotype Correlations Created: 08/04/09 @ 13:14:54 \| Last updated: 08/08/09 @ 18:57:58 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: 83 times \| Downloaded: 26 times Tags: affymetrix \| african trypanosomiasis \| cattle \| data-driven \| disease \| entrez \| genotype \| Kegg Pathways \| KeggID \| link-integration \| microarray \| mouse \| pathway \| pathway-driven \| phenotype \| sleeping sickness \| swissprot \| uniprot \| web services	View Download

Files (5)

Uploader: Paul Fisher	A Taverna Users Guide Created: 04/08/08 @ 17:40:21 Credits: Paul Fisher Katy Wolstencroft Franck Tanoh License: Creative Commons Attribution-Share Alike 3.0 Unported License No description File type: PowerPoint presentation Rating: 0.0 / 5 (0 ratings) \| Comments: 0 \| Viewed: 80 times \| Downloaded: 87 times Tags: bioinformatics \| microarray \| mining \| neuroscience \| newcastle \| sleeping sickness \| summary \| web services	View Download
Uploader: Suza Adam, Rapiddiscovery.biz	LIFEsparks biotechnology network Created: 19/10/08 @ 11:05:10 \| Last updated: 19/10/08 @ 11:12:58 Credits: Suza Adam, Rapiddiscovery.biz License: Creative Commons Attribution-Share Alike 3.0 Unported License The LIFEsparks biopartnering social forum aims to boost the commercial success of Southern African initiatives and start-up companies focused the life sciences sector (biotechnology and medical devices), vis-a-vis allowing participants to share ideas, knowledge and to present their business and or investment opportunities to potential partners and funders. File type: JPEG image Rating: 0.0 / 5 (0 ratings) \| Comments: 0 \| Viewed: 45 times \| Downloaded: 21 times Tags: africa \| agricultural biotechnology \| animal biotechnology \| biofuels \| bioinformatics \| biopartnering \| biotech funding \| biotech investment \| biotech startup \| biotechnology \| bloemfontein \| cape town \| cell therapy \| clinical trails \| clinical trials \| diagnostics \| drug development \| durban \| environmental biotechnology \| escience \| food technology \| forest biotechnology \| green plastics \| industrial sustainability \| johannesburg \| life sciences \| medical devices \| microarray \| nanobiotechnology \| personalised medicine \| pharmacology \| phytopharma \| pretoria \| professional network \| projects \| r&d \| rapiddiscovery.biz \| rapidremedial.biz \| research \| social media \| sosial network \| south africa \| suza adam \| therapeutics \| vaccines \| venture capital	View Download
Uploader: Paul Fisher	Tir1 QTL - Day 3 Microarray intersecting pathways Created: 08/04/09 @ 17:56:10 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 3 differentially expressed genes File type: Excel workbook Rating: 0.0 / 5 (0 ratings) \| Comments: 0 \| Viewed: 14 times \| Downloaded: 16 times Tags: african trypanosomiasis \| expression \| gene \| microarray \| qtl \| 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: 18 times \| Downloaded: 20 times Tags: affymetrix \| african trypanosomiasis \| gene \| microarray \| pathway \| qtl \| sleeping sickness	View Download
Uploader: Peter Li	Taverna microarray BMC Bioinformatics paper Created: 04/02/10 @ 11:35:51 Credits: Peter Li License: Creative Commons Attribution-Share Alike 3.0 Unported License No description File type: Adobe PDF Rating: 0.0 / 5 (0 ratings) \| Comments: 0 \| Viewed: 22 times \| Downloaded: 17 times Tags: microarray \| pdf	View Download

Workflows (20)

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 (1 rating) | Versions: 4 | Reviews: 0 | Comments: 0 | Citations: 0

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Taverna 1

Original Uploader

Paul Fisher

KEGG pathways common to both QTL and microarray based investigations (v3)

Created: 24/11/09 @ 17:14:43 | Last updated: 03/12/09 @ 15:28:49

License: Creative Commons Attribution-No Derivative Works 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. Example input for this workflow is given below (as newline separated values). qt...

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Taverna 1

Original Uploader

Peter Li

Query Maxd microarray database (v1)

Created: 14/11/07 @ 16:01:50 | Last updated: 22/11/07 @ 12:06:32

Credits: Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Retrieves data from the maxd database given name of data set

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Taverna 1

Original Uploader

Peter Li

Mapping microarray data onto metabolic pathways (v1)

Created: 14/11/07 @ 16:51:26 | Last updated: 22/11/07 @ 10:39:32

Credits: Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This workflow maps microarray data onto metabolic pathway diagrams represented as SBML models drawn using Cell Designer. To run this workflow requires libsbml to be installed into taverna - see http://www.mcisb.org/software/taverna/libsbml/index.html

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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: 222 times | Downloaded: 5 times

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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

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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...

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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 ...

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Taverna 1

Original Uploader

Peter Li

Identification of differential genes using t-tests by R (v2)

Created: 15/04/08 @ 15:37:42 | Last updated: 01/07/08 @ 17:21:18

Credits: Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This workflow starts by retrieving the names of microarray datasets from the Maxd database. The user has to select sets of control and test data for analysis using t-tests by R. A list of significant differentially expressed genes is then analysed using the Go Term Finder tool which generates a list of GO terms associated with the genes. A CSV file containing the list of significant genes is also generated.

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Taverna 1

Original Uploader

Peter Li

Identification of differential genes using the LIMMA Bioconductor package within R (v1)

Created: 02/07/08 @ 11:24:12 | Last updated: 02/07/08 @ 11:28:21

Credits: Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This workflow starts by retrieving the names of microarray datasets from the Maxd database. The user has to select sets of control and test data which are then analysed by the LIMMA Bioconductor package in an R script. This produces a list of significant differentially expressed genes which is then analysed using the Go Term Finder tool to generate a PDF report of the common GO terms associated with the genes. A CSV file containing the list of sign...

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Taverna 1

Original Uploader

Paul Fisher

Mouse Microarray Analysis (v3)

Created: 03/10/07 @ 18:36:05 | Last updated: 03/12/09 @ 16:20:33

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This workflow takes in probesets from and AffyMetrix micorarray experiment and returns: the genes ; gene start and end positions; chromosome where genes reside; ensembl trasncripts; SwissProt ids; affy probeset identifiers for chips Mouse430_2 and Mouse430a_2. Example ids from the Mouse430_2 affymetrix array are as follows (newline separated): 1447227_at 1440624_at 1436240_at 1454904_at 1435665_at 1418148_at 1429831_at

Rating: 5.0 / 5 (1 rating) | Versions: 3 | Reviews: 0 | Comments: 1 | Citations: 1

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Taverna 1

Original Uploader

Wei Tan

hierarchical microarray clustering (v1)

Created: 05/12/08 @ 18:31:53 | Last updated: 05/12/08 @ 20:33:37

Credits: Wei Tan

License: Creative Commons Attribution-Share Alike 3.0 Unported License

To illustrate our caGrid plug-in’s application, we tested it with a microarray hierarchical clustering workflow that involves services hosted at multiple institutions. Microarrays are a high-throughput technology used to measure the expression of tens of thousands of genes in different tissues or cells. Scientists represent the data from each microarray via a vector (profile) in which each element represents a gene’s expression level. They use clustering analysis to identify sim...

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Taverna 1

Original Uploader

Wassinki

Mapping OligoNucleotides to an assembly (v7)

Created: 13/02/09 @ 09:05:35 | Last updated: 13/02/09 @ 09:08:20

Credits: Wassinki Pieter Neerincx

Attributions: Blat against ENSEMBLE Danio_rerio_Genome BlatBlastCombi Blast against ENSEMBLE Danio_rerio_Genome AppendToFile Test Input for Mapping oligonucleotides to an assembly Input for Mapping oligonucleotides to an assembly

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Version info The former version of the workflow expected that results from BioMART only report transcripts when the query (the probe in our case) are entirely encapsulated in an exon of that transcript. However, the BioMart service also returns transcripts when the query is not or only partially overlapping with an exon in the stretch on the assembly on which a transcript is defined. This resulted in too many oligos classified as having multiple transcripts or having multiple genes. ...

Rating: 0.0 / 5 (0 ratings) | Versions: 7 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 248 times | Downloaded: 46 times

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biomart
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BLAST
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blat
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ensembl
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microarray
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r
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rshell

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Taverna 2

Original Uploader

Wei Tan

Lymphoma type prediction based on microarray data (v7)

Created: 11/05/10 @ 19:04:30 | Last updated: 11/05/10 @ 19:04:32

Credits: Wei Tan Madduri Stian Soiland-Reyes

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Scientific value Using gene-expression patterns associated with DLBCL and FL to predict the lymphoma type of an unknown sample. Using SVM (Support Vector Machine) to classify data, and predicting the tumor types of unknown examples. Steps Querying training data from experiments stored in caArray. Preprocessing, or normalize the microarray data. Adding training and testing data into SVM service to get classification result.

Rating: 0.0 / 5 (0 ratings) | Versions: 7 | Reviews: 0 | Comments: 0 | Citations: 2

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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.

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Taverna 2

Original Uploader

Wei Tan

caArray data retrieving (v1)

Created: 23/11/09 @ 18:09:47

Credits: Wei Tan

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Query all the gene expression data in a caArray experiment. Returns a evenly divided gene expression data set with corresponding class information. They ca be later used as training and test data set in many classification algorithms.Query all the gene expression data in a caArray experiment. Returns a evenly divided gene expression data set with corresponding class information. They can be later used as training and test data set in many classification algorithms.

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Taverna 2

Original Uploader

Wei Tan

genePattern data preprocessing (v2)

Created: 24/05/10 @ 22:42:38 | Last updated: 24/05/10 @ 22:42:39

Credits: Wei Tan

License: Creative Commons Attribution-Share Alike 3.0 Unported License

preprocess data set using genePattern preProces service, the input should be in genePattern STATML format. Configuration parameters can be adjusted by changing the default preprocess data set using genePattern preProces service, the input should be in genePattern STATML format.preprocess data set using genePattern preProces service, the input should be in genePattern STATML format. Configuration parameters can be adjusted by changing the string constants.

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Taverna 2

Original Uploader

Peter Li

Calculating frequencies of gene expression levels using microarray data in MaxD (v1)

Created: 15/03/10 @ 08:43:31

Credits: Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This workflow retrieves data from the MaxD microarray database and calculates the frequencies of gene expression levels using an R script

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beanshell
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database
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expression
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gene
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image
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maxd
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microarray
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r
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xpath

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Taverna 2

Original Uploader

Wei Tan

Query caArray data service and retrieving files (v2)

Created: 24/05/10 @ 22:55:57 | Last updated: 24/05/10 @ 22:55:58

Credits: Wei Tan

License: Creative Commons Attribution-Share Alike 3.0 Unported License

need to install Taverna 2 caGrid integration suite from http://www.mcs.anl.gov/~wtan/t2/ and get a cagrid Dorian account (see http://wiki.cagrid.org/display/caGrid13/Home)

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Taverna 2

Original Uploader

Wei Tan

A simple CQL query workflow in caGrid (v1)

Created: 24/05/10 @ 23:52:05 | Last updated: 25/05/10 @ 19:20:30

Credits: Wei Tan

License: Creative Commons Attribution-Share Alike 3.0 Unported License

1. CQL is a language to query data from caGrid/caBIG services. This workflow is tested with Taverna 2.1.2 and the caGrid Workflow Suite downloadable from http://www.mcs.anl.gov/~wtan/t2/. 2.More information regarding CQL can be found from http://wiki.cagrid.org/display/dataservices. 3. Sample input (95) is provided in the workflow. It is to query all the hybridization data within a microarray experiment whose id is 95.

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Tag Results

Items tagged with "microarray" (29)