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Items tagged with "phenotype" (7)

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Mariebrown

metabolomics

Created: Thursday 29 November 2007 @ 11:50:47 (GMT)

Data analysis and bioinformatics of metabolomic studies

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Workflows (6)

Taverna 1

Original Uploader

Paul Fisher

Mouse Pathways and Gene annotations for QTL Phenotype (v3)

Created: 03/10/07 @ 18:36:02 | Last updated: 20/02/08 @ 16:05:45

License: Creative Commons Attribution-Share Alike 3.0 License

This workflow searches for genes which reside in a QTL (Quantitative Trait Loci) region in the mouse, Mus musculus. The workflow requires an input of: a chromosome name or number; a QTL start base pair position; QTL end base pair position. 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 path...

Rating: 4.5 / 5 (2 ratings) | Versions: 3 | Reviews: 0 | Comments: 2 | Citations: 1

Viewed: 1439 times | Downloaded: 1455 times

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Taverna 1

Original Uploader

Paul Fisher

HUMAN Microarray CEL file to candidate pathways (v4)

Created: 03/10/07 @ 18:35:55 | Last updated: 04/04/08 @ 12:14:21

License: Creative Commons Attribution-NoDerivs 3.0 License

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 ...

Rating: 5.0 / 5 (1 rating) | Versions: 4 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 1755 times | Downloaded: 1646 times

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Taverna 1

Original Uploader

Paul Fisher

Entrez Gene to KEGG Pathway (v2)

Created: 03/10/07 @ 18:36:00 | Last updated: 13/11/07 @ 16:16:10

License: Creative Commons Attribution 3.0 License

This workflow takes in Entrez gene ids then adds the string "ncbi-geneid:" to the start of each gene id. These gene ids are then cross-referenced to KEGG gene ids. Each KEGG gene id is then sent to the KEGG pathway database and its relevant pathways returned.

Rating: 4.7 / 5 (3 ratings) | Versions: 2 | Reviews: 0 | Comments: 1 | Citations: 0

Viewed: 1592 times | Downloaded: 986 times

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Taverna 1

Original Uploader

Paul Fisher

KEGG pathways common to both QTL and microarray based investigations (v2)

Created: 03/10/07 @ 18:35:58 | Last updated: 13/11/07 @ 16:22:14

License: Creative Commons Attribution-NoDerivs 3.0 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: 2 | Reviews: 0 | Comments: 0 | Citations: 1

Viewed: 891 times | Downloaded: 735 times

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Taverna 1

Original Uploader

Paul Fisher

Pathways from Diff Expressed Genes (v3)

Created: 03/10/07 @ 18:36:05 | Last updated: 11/07/08 @ 10:52:01

License: Creative Commons Attribution-Share Alike 3.0 License

This workflow takes in probesets from and AffyMetrix micorarray experiment and returns: the genes in the QTL; gene start and end positions; chromosome where genes reside; ensembl trasncripts; SwissProt ids; affy probeset identifiers for chips Mouse430_2 and Mouse430a_2.

Rating: 5.0 / 5 (1 rating) | Versions: 3 | Reviews: 0 | Comments: 1 | Citations: 1

Viewed: 1156 times | Downloaded: 1078 times

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Taverna 1

Original Uploader

Paul Fisher

Pathway to Pubmed (v2)

Created: 09/03/08 @ 15:03:12 | Last updated: 08/07/08 @ 12:13:06

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 License

This workflow takes in a list of KEGG pathway descriptions and searches the PubMed database for corresponding articles. Any matches to the pathways are then retrieved (abstracts only). These abstracts are then returned to the user.

Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 771 times | Downloaded: 535 times

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