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Items tagged with "expression" (12)

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Paul Fisher

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Tir1 QTL - Day 3 Microarray intersecting pathways

Created: 2009-04-08 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

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Paul Fisher

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Human Probeset data from Affymetrix

Created: 2011-04-01 09:08:45 | Last updated: 2011-04-01 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

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Taverna 1

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Paul Fisher

Mouse Microarray Analysis (3)

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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

Created: 2007-10-03 | Last updated: 2009-12-03

Taverna 1

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Paul Fisher

Human Microarray Analysis (1)

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

Created: 2008-02-08 | Last updated: 2009-12-03

Credits: Paul Fisher

Taverna 2

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Peter Li

Calculating frequencies of gene expression... (1)

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

Created: 2010-03-15

Credits: Peter Li

Taverna 2

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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

Taverna 2

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Kristina Hettne

Annotate a gene list with disease concepts (1)

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Purpose: Currently, this workflow takes a list of genes and a concept set as input, calculates the matching score between these and finds the concept that contributes the most to the match. Author comments: The workflow is in Beta stage. It runs, but needs more testing with different parameter settings. This workflow can be used together with other workflows in this pack: http://www.myexperiment.org/packs/368 for functional gene annotation and knowledge discovery.

Created: 2013-02-06

Credits: Kristina Hettne Reinout van Schouwen Marco Roos BioSemantics

Attributions: SNPs to Concept Set through Concept Profile Matching v2

geneXplain type

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geneXplain

Compute differentially expressed genes (1)

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This workflow is designed to identify up-regulated, down-regulated and non-changed genes for experimental data with three and more data points for each experiment and control. As input, normalized data with any types of IDs (Ensembl, gene symbols, EMBL, RefSeq) can be submitted.In the next step, p-values for up- and down-regulated probes are calculated for all probes using the “Up and Down Identification” analysis. This analysis applies Student’s T-test for p-value cal...

Created: 2013-11-13 | Last updated: 2015-04-17

Credits: geneXplain

Taverna 2

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Katy Wolstencroft

ImportConvertEnsembl (1)

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This workflow accepts a spreadsheet file as input and extracts a list of ENSEMBL Gene IDs from column A. The hsapiens_gene_ensembl service converts these IDs to Entrez_geneIds

Created: 2014-09-05

Credits: Katy Wolstencroft

Taverna 2

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Kristina Hettne

AllPW2ENS (2)

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This workflow uses the WikiPathways Webservice/API to query to retrieve all ENSEMBL identifers for all pathways and merge them into one, unique list.

Created: 2015-10-02 | Last updated: 2015-10-12

Credits: Kristina Hettne Eleni

Taverna 2

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Kristina Hettne

GetWikiPWByENS (2)

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This workflow uses the WikiPathways Webservice/API to query for pathways containing a specific ENSEMBL identifier. The mapping service behind WikiPathways takes care of the identifier mapping, making sure that all relevant results are found even if they were originally reported using a different identifier scheme.