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Items tagged with "microarray" (36)

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Files (6)
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Blob LIFEsparks biotechnology network

Created: 19/10/08 @ 11:05:10 | Last updated: 19/10/08 @ 11:12:58

Credits: User Suza Adam

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

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Blob Tir1 QTL - Day 3 Microarray intersecting pathways

Created: 08/04/09 @ 17:56:10

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 3 differentially expressed genes

File type: Excel workbook

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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 Taverna microarray BMC Bioinformatics paper

Created: 04/02/10 @ 11:35:51

Credits: User Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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File type: Adobe PDF

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Blob Trichuriasis Induced Colitis

Created: 16/02/11 @ 15:16:17 | Last updated: 16/02/11 @ 15:16:24

Credits: User Paul Fisher

Attributions: Workflow Pathways and Gene annotations for RefSeq ids Workflow KEGG pathways common to both QTL and microarray based investigations Workflow Pathways and Gene annotations for QTL region Workflow Pathway and Gene to Pubmed

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This zip file contains the results of workflow runs for: identifying genes in each of the 7 QTL regions for Trichuris muris infection; identifying genes differentially expressed in mice challenged with Trichuris muris; and Text mining results (including cosine vector scores and Term Enrichment values).

File type: Trident (Package)

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Workflows (25)
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 KEGG pathways common to both QTL and micro... (3)

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

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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.   Example input for this workflow is given below (as newline separated values). qt...

Rating: 0.0 / 5 (0 ratings) | Versions: 3 | Reviews: 0 | Comments: 0 | Citations: 1

Viewed: 319 times | Downloaded: 136 times

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Original Uploader

Workflow Query Maxd microarray database (1)

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

Credits: User Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Retrieves data from the maxd database given name of data set

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Original Uploader

Workflow Mapping microarray data onto metabolic pat... (1)

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

Credits: User Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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

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

Viewed: 575 times | Downloaded: 181 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 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 Identification of differential genes using... (2)

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

Credits: User Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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.

Rating: 5.0 / 5 (1 rating) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 1

Viewed: 483 times | Downloaded: 163 times

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Original Uploader

Workflow Identification of differential genes using... (1)

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

Credits: User Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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...

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

Viewed: 622 times | Downloaded: 234 times

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Original Uploader

Workflow Mouse Microarray Analysis (3)

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

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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

Viewed: 561 times | Downloaded: 141 times

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Original Uploader

Workflow hierarchical microarray clustering (1)

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

Credits: User Wei Tan

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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...

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

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Original Uploader

Workflow Mapping OligoNucleotides to an assembly (7)

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

Credits: User Wassinki User Pieter Neerincx

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

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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: 627 times | Downloaded: 115 times

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Original Uploader

Workflow Lymphoma type prediction based on microar... (7)

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

Credits: User Wei Tan User Ravi User Stian Soiland-Reyes

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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: 5.0 / 5 (1 rating) | Versions: 7 | Reviews: 0 | Comments: 0 | Citations: 3

Viewed: 685 times | Downloaded: 254 times

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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 caArray data retrieving (1)

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

Credits: User Wei Tan

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 3 | Citations: 0

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Original Uploader

Workflow genePattern data preprocessing (2)

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

Credits: User Wei Tan

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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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Original Uploader

Workflow Calculating frequencies of gene expression... (1)

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

Credits: User Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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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Original Uploader

Workflow Query caArray data service and retrieving ... (2)

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

Credits: User Wei Tan

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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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Original Uploader

Workflow A simple CQL query workflow in caGrid (1)

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

Credits: User Wei Tan

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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.

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

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Original Uploader

Workflow Principle Component Analysis (PCA) over mi... (1)

Created: 10/09/10 @ 23:45:05 | Last updated: 10/09/10 @ 23:51:03

Credits: User Wei Tan

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Principle Component Analysis (PCA) over microarray data. Data is uploaded through caGrid transfer ultility.

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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

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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 Gene to Pubmed (4)

Created: 08/02/11 @ 13:04:06 | Last updated: 10/02/11 @ 16:01:41

Credits: User Paul Fisher

Attributions: Workflow Cosine vector space Workflow Extract Scientific Terms Workflow Rank Phenotype Terms Workflow Cosine vector space Workflow Rank Phenotype Terms Workflow Pathway to Pubmed Workflow Extract Scientific Terms

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow takes in a list of gene names and searches the PubMed database for corresponding articles. Any matches to the genes are then retrieved (abstracts only). These abstracts are then returned to the user.

Rating: 0.0 / 5 (0 ratings) | Versions: 4 | Reviews: 0 | Comments: 0 | Citations: 0

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Original Uploader

Workflow Pathways and Gene annotations forQTL region (1)

Created: 24/03/11 @ 15:14:48 | Last updated: 24/03/11 @ 15:37:48

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow searches for genes found from a set of differentially expressed probestes, in Human, Homo sapiens. The workflow requires an input human affymetrix probeset identifiers. 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 database.

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

Viewed: 31 times | Downloaded: 13 times

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Packs (5)
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Pack Microarray data analysis using R


Created: 02/07/08 @ 11:30:06 | Last updated: 04/02/10 @ 11:41:11

No description

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Pack useful_for_sysmo


Created: 17/12/08 @ 12:31:48 | Last updated: 10/06/09 @ 09:43:20

These workflows have been collected as potentially useful protocols for the sysmo consortium

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Pack 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"  

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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 Trichuriasis induced Colitis


Created: 16/02/11 @ 12:49:21 | Last updated: 16/02/11 @ 15:26:36

This pack contains the workflows and data relating to Trichuriasis induced colitis.

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Comments: 0 | Viewed: 22 times | Downloaded: 3 times

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