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Items tagged with "pathways" (10)

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Created: Thursday 29 November 2007 @ 11:46:44 (GMT)

For people interested in doing SBML-related stuff in workflows

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Workflow HUMAN Microarray CEL file to candidate pathways (v4)

Created: 03/10/07 @ 18:35:55 | Updated: 04/04/08 @ 12:14:20

License: Creative Commons Attribution-NoDerivs 3.0 License

Microarray_cel_file_to_candidate_pathways_17032_4
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: 1365 times | Downloaded: 1293 times

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Workflow Entrez Gene to KEGG Pathway (v2)

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

License: Creative Commons Attribution 3.0 License

Entrez_gene_to_kegg_pathway_7493
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: 1260 times | Downloaded: 756 times

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

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

License: Creative Commons Attribution-NoDerivs 3.0 License

Kegg_pathways_common_to_both_qtl_and_microarray_based_investigations_27627
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

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Workflow Mouse Pathways and Gene annotations for QTL Phenotype (v3)

Created: 03/10/07 @ 18:36:02 | Updated: 20/02/08 @ 16:05:44

License: Creative Commons Attribution-Share Alike 3.0 License

Pathways_and_gene_annotations_for_qtl_phenotype_28303_3
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

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Workflow kegg_gene_to_swissprot_identifier (v1)

Created: 27/11/07 @ 11:53:11 | Updated: 28/11/07 @ 12:58:38

Credits: User Sirisha Gollapudi

License: Creative Commons Attribution-Share Alike 3.0 License

Kegg_gene_to_swissprot_identifier_26120
Takes a KEGG gene identifier, e.g. sce:YAL038W (yeast pyruvate kinase) and converts to the corresponding Swissprot identifier.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 1 | Citations: 0

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Workflow Microarray CEL file to candidate pathways (v2)

Created: 08/02/08 @ 14:17:23 | Updated: 14/05/08 @ 15:43:16

Credits: User Paul Fisher User Saeedeh

License: Creative Commons Attribution-Share Alike 3.0 License

Microarray_cel_file_to_candidate_pathways_1844_2
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

Viewed: 598 times | Downloaded: 1 time

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Workflow Human Pathways from Diff Expressed Genes (v1)

Created: 08/02/08 @ 14:30:17 | Updated: 08/02/08 @ 14:30:17

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 License

Human_pathways_from_diff_expressed_genes_4391_1
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. The final output of the workflow is a list of candidate pathways which are linked to the genes expressed in the microarray data

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 1 | Citations: 0

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Workflow Pathway to Pubmed (v2)

Created: 09/03/08 @ 15:03:11 | Updated: 08/07/08 @ 12:13:06

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 License

Pathway_to_pubmed_25676_2
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: 566 times | Downloaded: 373 times

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Workflow Escherichia coli : From cDNA Microarray Raw Data to Pathways and Published Abstracts (v1)

Created: 08/05/08 @ 15:25:29 | Updated: 12/05/08 @ 09:01:37

Credits: User Saeedeh User Paul Fisher

Attributions: Workflow HUMAN Microarray CEL file to candidate pathways

License: Creative Commons Attribution-Share Alike 3.0 License

Escherichia_coli___from_cdna_microarray_raw_data_to_pathways_and_published_abstracts_6837_1
This workflow takes in a CDNA raw file and a normalisation method then returns a series of images/graphs which represent the same output obtained using the R and bioconductor. 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 changes in the microarray data. By identifying the candidate pathways, more detailed...

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 338 times | Downloaded: 182 times

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