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Showing 11 results. Use the filters on the left and the search box below to refine the results.
Tag: microarray User: Paul Fisher Licence: by-sa

Workflow 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

Workflow Microarray CEL file to candidate pathways (2)

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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...

Created: 2008-02-08 | Last updated: 2009-02-13

Credits: User Paul Fisher User Saeedeh

Workflow Human Microarray Analysis (1)

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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  

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

Credits: User Paul Fisher

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Blob Tir1 QTL - microarray day 7 intersecting pathways

Created: 2009-04-08 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

Comments: 0 | Viewed: 54 times | Downloaded: 43 times

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Blob Tir1 QTL - Day 3 Microarray intersecting pathways

Created: 2009-04-08 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

Comments: 0 | Viewed: 47 times | Downloaded: 36 times

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Workflow Pathways and Gene annotations forQTL region (1)

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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.

Created: 2011-03-24 | Last updated: 2011-03-24

Credits: User Paul Fisher

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Blob Trichuriasis Induced Colitis

Created: 2011-02-16 15:16:17 | Last updated: 2011-02-16 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)

Comments: 0 | Viewed: 28 times | Downloaded: 20 times

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Workflow Gene to Pubmed (4)

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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.

Created: 2011-02-08 | Last updated: 2011-02-10

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

Workflow 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: User Paul Fisher

Workflow 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: User Paul Fisher

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