myExperiment - Tags - gene expression

Workflows (6)

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... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 177 times \| Downloaded: 72 times Tags (8): cabig \| cagrid \| cancer research \| clustering \| gene expression \| globus \| grid service \| microarray	View Download (v1)
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 Ravi 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: 5.0 / 5 (1 rating) \| Versions: 7 \| Reviews: 0 \| Comments: 0 \| Citations: 3 Viewed: 583 times \| Downloaded: 227 times Tags (11): cabig \| cagrid \| cancer research \| classification \| gene expression \| globus \| grid service \| lymphoma \| lymphoma workflow \| microarray \| support vector machine	View Download (v7)
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 Marco Roos	Gene expression interpretation by the Global Test (v1) Created: 26/04/11 @ 08:31:51 \| Last updated: 26/04/11 @ 08:31:52 Credits: Marco Roos License: Creative Commons Attribution-Share Alike 3.0 Unported License 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... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 19 times \| Downloaded: 0 times Tags (8): biosemantics \| e-science \| entrez \| gene expression \| GO \| normalization \| phenotype \| text_mining	View

Packs (2)

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

Comments: 0 | Viewed: 83 times | Downloaded: 7 times

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Creator:

Paul Fisher

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.

5 items in this pack

Comments: 0 | Viewed: 15 times | Downloaded: 2 times

Tags:

annotation
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chromosome
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controlled vocabulary
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cosine vector space
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data integration
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data-driven
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dresden
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efetch
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enrichment
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ensembl
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entity recognition
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esearch
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evidence
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gene expression
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gene identifier
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genotype
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kegg
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Kegg Pathways
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KeggID
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literature
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loci
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locus
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medline
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microarray
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mining
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pathway
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pathway-driven
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phenotype
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pubmed
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qtl
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quanitative
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ranking
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re-use
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significance
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term
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term extraction
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terms
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text
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text mining
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text mining; term extraction; entity recognition
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trait
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trichuris muris

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Files (4)

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 Rating: 0.0 / 5 (0 ratings) \| Comments: 0 \| Viewed: 6 times \| Downloaded: 4 times Tags: bioinformatics \| gene expression \| image processing \| prostack \| segmentation \| workflow	View Download
Uploader: Paul Fisher	Trichuriasis Induced Colitis Created: 16/02/11 @ 15:16:17 \| Last updated: 16/02/11 @ 15:16:24 Credits: Paul Fisher Attributions: Pathways and Gene annotations for RefSeq ids KEGG pathways common to both QTL and microarray based investigations Pathways and Gene annotations for QTL region 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) Rating: 0.0 / 5 (0 ratings) \| Comments: 0 \| Viewed: 7 times \| Downloaded: 5 times Tags: gene expression \| genotype \| Kegg Pathways \| microarray \| pathway-driven \| phenotype \| pubmed \| qtl \| trait \| trichuris muris	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 "gene expression" (12)