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Items tagged with "gene expression" (5)

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Packs (1)

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 (1)

Uploader:

Konstantin Kozlov

ProStack Screencast: Segmentation of Images of Gene Expression Patterns

Created: 20/05/10 @ 19:48:40

Credits: Konstantin Kozlov

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

ProStack (Processing of Stacks) is a platform for image processing and analysis. It implements various image processing methods as separate modules, that can be joined in a complex image processing scenario by use of a graphical user interface. This video demonstrates the workflow for extraction of quantitative information on gene expression from confocal images. ProStack home page: urchin.spbcas.ru/downloads/ProStack/ProStack.htm Download:sourceforge.net/projects/prostack/

File type: AVI video

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Workflows (3)

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 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.

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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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