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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

Original Uploader

Paul Fisher

Perfrom a text based search through PubMed (v3)

Created: 03/10/07 @ 18:36:08 | Last updated: 02/08/08 @ 14:35:11

License: Creative Commons Attribution-NoDerivs 3.0 License

This workflow takes in a number of search terms in which to perform a search over the PubMed literature database. These search terms may be input as if entered in the web based version of PubMed. The output from this workflow is a list of PubMed identifiers in xml based format

Rating: 3.0 / 5 (2 ratings) | Versions: 3 | Reviews: 0 | Comments: 1 | Citations: 0

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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

Original Uploader

Paul Fisher

Microarray CEL file to candidate pathways (v2)

Created: 08/02/08 @ 14:17:23 | Last updated: 14/05/08 @ 15:43:23

Credits: Paul Fisher Saeedeh

License: Creative Commons Attribution-Share Alike 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: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0

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