Workflows

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

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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.

Created: 2010-05-11 | Last updated: 2010-05-11

Credits: Wei Tan Ravi Stian Soiland-Reyes

hierarchical microarray clustering (1)

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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...

Created: 2008-12-05 | Last updated: 2008-12-05

Credits: Wei Tan

Search for Gene Expression Images using an... (1)

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This is a simple workflow demonstrating how to integrate multiple linked data sources using restful services in Taverna. In this workflow it first searches for all possible gene names for a query gene from FlyBase repository, an authorative genetic database for Drosophila research, and then it uses returned gene names to search for gene expression images from Oxford FlyTED image repository. Two Restful services were used: One for retrieving all flybase features matching a querying ge...

Created: 2012-05-04 | Last updated: 2012-05-08

Credits: Junzhao

Get Alternative Gene Names for a Drosophil... (1)

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This is a simple workflow testing running a restful service in Taverna. This restful service http://www.open-biomed.org.uk/service/flybase/features/name/{name} is part of the flykit/flybase services http://code.google.com/p/open-biomed/wiki/Flybase, which is built using the Talis Puelia Linked Data API (http://code.google.com/p/puelia-php/). We want to use this simple workflow to test the idea of bridging linked data and scientific workflows using Restful services. A test input gene name...

Created: 2012-05-04 | Last updated: 2012-05-04

Credits: Junzhao

Get FlyTED Gene Expression Images for a Ge... (1)

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This is a simple workflow testing running a restful service in Taverna. This restful service http://www.open-biomed.org.uk/service/flyted/records/probe/{probe} is part of the flykit/flyted services http://code.google.com/p/open-biomed/wiki/Flyted, which is built using the Talis Puelia Linked Data API (http://code.google.com/p/puelia-php/). We want to use this simple workflow to test the idea of bridging linked data and scientific workflows using Restful services. A test input gene name can ...

Created: 2012-05-04 | Last updated: 2012-05-04

Credits: Junzhao

Gene expression interpretation by the Glob... (1)

This workflow adds meaning to gene expresion values by performing a standard and a literature weighted Global Test. Gene expression is expected to be from Affymetrix microarrays, for which an RMA normalization and entrez Gene ID mapping/summation is performed. Original workflow is by Dennis Leenheer, edits by Marco Roos. Scripts by Kristina Hettne, acknowledging Rob Jellier, Jelle Goeman, and Peter-Bram 't Hoen. The workflow was created for the LUMC BioSemantics group, part of the Human Gen...

Created: 2011-04-26 | Last updated: 2011-04-26

Credits: Marco Roos

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

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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

Created: 2010-11-15 | Last updated: 2010-11-15

Credits: Paul Fisher

Pathways and Gene annotations for RefSeq ids (1)

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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.

Created: 2010-11-15 | Last updated: 2010-11-15

Credits: Paul Fisher