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Items tagged with "disease" (10)

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Pack Towards Genotype-Phenotype Correlations

Created: 08/04/09 @ 13:14:54 | Last updated: 08/08/09 @ 18:57:58

It is increasingly common to combine Microarray and Quantitative Trait Loci data to aid the search for candidate genes responsible for phenotypic variation. Workflows provide a means of systematically processing large datasets, and represent a framework for the re-use and the explicit declaration of experimental methods. In this pack is a paper which describes the issues facing the manual analysis of microarray and QTL data for the discovery of candidate genes underlying complex phenotypes.&n...

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Workflows (9)
Taverna 1

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Workflow BioAID_DiseaseDiscovery (v3)

Created: 15/12/08 @ 20:46:09 | Last updated: 15/12/08 @ 20:47:50

Credits: User Marco Roos Network-member AID

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Bioaid_diseasediscoveryworkflow_070904_1__1_
This workflow finds disease relevant to the query string via the following steps: 1. A user query: a list of terms or boolean query - look at the Apache Lucene project for all details. E.g.: (EZH2 OR "Enhancer of Zeste" +(mutation chromatin) -clinical); consider adding 'ProteinSynonymsToQuery' in front of the input if your query is a protein. 2. Retrieve documents: finds 'maximumNumberOfHits' relevant documents (abstract+title) based on query (the AIDA service inside is based on Apa...

Rating: 4.0 / 5 (2 ratings) | Versions: 3 | Reviews: 0 | Comments: 2 | Citations: 0

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Taverna 1

Original Uploader

Workflow KEGG pathways common to both QTL and microarray based investigations (v3)

Created: 24/11/09 @ 17:14:43 | Last updated: 03/12/09 @ 15:28:49

License: Creative Commons Attribution-No Derivative Works 3.0 Unported License

Kegg_pathways_common_to_both_qtl_and_microarray_based_investigations
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.   Example input for this workflow is given below (as newline separated values). qt...

Rating: 0.0 / 5 (0 ratings) | Versions: 3 | Reviews: 0 | Comments: 0 | Citations: 1

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Taverna 1

Original Uploader

Workflow Pathways and Gene annotations for QTL region (v5)

Created: 19/11/09 @ 18:18:52 | Last updated: 20/11/09 @ 10:33:25

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Pathways_and_gene_annotations_forqtl_region
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: 5 | Reviews: 0 | Comments: 2 | Citations: 1

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Taverna 1

Original Uploader

Workflow Mouse Microarray Analysis (v3)

Created: 03/10/07 @ 18:36:05 | Last updated: 03/12/09 @ 16:20:33

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Pathways_from_diff_expressed_genes_22895_3
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

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

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Taverna 1

Original Uploader

Workflow BioAID_ProteinToDiseases (v1)

Created: 14/11/07 @ 12:47:57 | Last updated: 15/11/07 @ 09:00:44

Credits: User Marco Roos User Martijn Schuemie Network-member AID

Attributions: Workflow BioAID_DiseaseDiscovery

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Bioaid_proteintodiseases_16160
This workflow was based on BioAID_DiseaseDiscovery, changes: expects only one protein name, adds protein synonyms). This workflow finds diseases relevant to the query string via the following steps: A user query: a single protein name Add synonyms (service courtesy of Martijn Scheumie, Erasmus University Rotterdam) Retrieve documents: finds relevant documents (abstract+title) based on query Discover proteins: extract proteins discovered in the set of relevant abstracts 5. Link proteins ...

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

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Taverna 1

Original Uploader

Workflow Gene annotation pipeline for the Graves disease scenario (v2)

Created: 03/10/07 @ 18:36:09 | Last updated: 22/11/07 @ 16:03:15

Credits: User Katy Wolstencroft User Peter Li

License: Creative Commons Attribution-No Derivative Works 3.0 Unported License

Gene_annotation_pipeline_for_the_graves_disease_scenario_19721
This is a revised workflow for the Graves disease scenario gene annotation pipeline used in the myGrid project. The workflow had to be re-written due to the loss of the services invoked in the original workflow.

Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 1 | Citations: 0

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Taverna 1

Original Uploader

Workflow Microarray CEL file to candidate pathways (v2)

Created: 08/02/08 @ 14:17:23 | Last updated: 13/02/09 @ 11:29:52

Credits: User Paul Fisher User Saeedeh

License: Creative Commons Attribution-Share Alike 3.0 Unported 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 ch...

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

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Taverna 1

Original Uploader

Workflow Human Microarray Analysis (v1)

Created: 08/02/08 @ 14:30:17 | Last updated: 03/12/09 @ 16:50:29

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Human_pathways_from_diff_expressed_genes_4391_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  

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

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Taverna 2

Original Uploader

Workflow Phenotype to Pubmed (v1)

Created: 05/07/10 @ 14:07:33 | Last updated: 05/07/10 @ 14:07:39

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Phneotype_to_pubmed
This workflow takes in a list of terms to search across the MEDLINE database (through PubMed).  Terms are passed to the eSearch function and searched for in PubMed. Those abstracts found are returned to the user via the eFetch service.

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

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