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Items tagged with "mouse" (15)

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Files (4)
Uploader

Blob Table of SNP sequenceing results

Created: 08/04/09 @ 13:29:32

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This file contains the results of re-sequencing the Daxx gene

File type: Word document

Rating: 0.0 / 5 (0 ratings) | Comments: 0 | Viewed: 800 times | Downloaded: 27 times

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Blob Kegg gene descriptions

Created: 08/04/09 @ 18:06:23 | Last updated: 10/08/09 @ 12:10:07

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This file contains a list of KEGG gene descriptions, for each KEGG gene identified within the Tir1 QTL region.

File type: Plain text

Rating: 0.0 / 5 (0 ratings) | Comments: 0 | Viewed: 27 times | Downloaded: 30 times

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Blob Gene Cosine Scores

Created: 10/08/09 @ 16:00:45

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This excel file contains a list of genes linked to the resistance to African trypanosomiasis in the mouse. Genes from the Tir1 QTL were used in a search through PubMed. The results were then correlated to the trypanosomiasis resistance phenotype. The higher the score (and ranking) the more related to the phenotype the gene is likely to be. This is based on the co-occurrence of terms within the gene and phentoype corpora.

File type: Excel workbook

Rating: 0.0 / 5 (0 ratings) | Comments: 0 | Viewed: 18 times | Downloaded: 0 times

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Blob Phenotype Concept Profile - Terms

Created: 11/08/09 @ 13:05:07 | Last updated: 11/08/09 @ 13:06:51

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This file contains a list of all terms extracted from the phenotype corpus, relating to African trypanosomiasis resistance in the mouse model. These terms were extracted using the following service: http://gopubmed4.biotec.tu-dresden.de/GoPubMedTermGenerationService/services/GoPubMedTermGeneration?wsdl These terms represent the concept profile for the phenotype.

File type: Plain text

Rating: 0.0 / 5 (0 ratings) | Comments: 0 | Viewed: 24 times | Downloaded: 0 times

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Workflows (9)
Original Uploader

Workflow Mouse Microarray Analysis (3)

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

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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

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

Viewed: 561 times | Downloaded: 141 times

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Original Uploader

Workflow Microarray CEL file to candidate pathways (2)

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

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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...

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

Viewed: 296 times | Downloaded: 5 times

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Original Uploader

Workflow Pathways and Gene annotations for QTL region (7)

Created: 19/11/09 @ 18:18:52 | Last updated: 07/09/12 @ 18:23:36

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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: 4.6 / 5 (10 ratings) | Versions: 7 | Reviews: 1 | Comments: 7 | Citations: 1

Viewed: 6121 times | Downloaded: 1014 times

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Original Uploader

Workflow Extract Scientific Terms (1)

Created: 10/08/09 @ 13:31:07 | Last updated: 10/08/09 @ 13:32:21

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow takes in a document containg text and removes any non-ascii characters. The cleaned text is then sent to a service in Dresden, to extract all scientific terms. These terms represent a concept profile for the input concpet. Any null values are also removed.

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

Viewed: 137 times | Downloaded: 0 times

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Original Uploader

Workflow Pathways and Gene annotations for QTL region (1)

Created: 15/11/10 @ 12:08:18 | Last updated: 16/11/10 @ 16:07:49

Credits: User Paul Fisher

Attributions: Workflow Pathways and Gene annotations for QTL region

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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

Viewed: 43 times | Downloaded: 14 times

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Original Uploader

Workflow Pathways and Gene annotations for RefSeq ids (1)

Created: 15/11/10 @ 12:25:01 | Last updated: 15/11/10 @ 12:28:12

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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.

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

Viewed: 85 times | Downloaded: 36 times

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Original Uploader

Workflow BiomartAndEMBOSSDisease (4)

Created: 27/01/11 @ 17:03:03 | Last updated: 04/09/12 @ 09:32:08

Credits: User Katy Wolstencroft User Alan Williams

Attributions: Workflow BiomartAndEMBOSSAnalysis

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow retrieves all genes on human chromosome 22 that are associated with a disease and aligns the upstream regions with mouse and rat homologues. The alignments are plotted and corresponding sequence ids are also returned. Using Biomart and EMBOSS soaplab services, This workflow retrieves a number of sequences from 3 species: mouse, human, rat; align them, and returns a plot of the alignment result. Corresponding sequence ids are also returned.

Rating: 0.0 / 5 (0 ratings) | Versions: 4 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 131 times | Downloaded: 74 times

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Original Uploader

Workflow Mouse Brain Image Analysis: General Linear... (1)

Created: 06/04/11 @ 01:52:56 | Last updated: 06/04/11 @ 01:53:01

Credits: User Pipeline

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Overview - General Linear Model The workflow runs voxelwise statistics on two populations of mice. Each of the populations has been scanned prior to injection of a label and at four subsequent timepoints.   Problem addressed by this workflow The workflow addresses several problems. First of all, it performs co-registration between the subjects from the two populations and at different timepoints. It then scales all images. Finally, it runs a multiple linear regression module t...

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

Viewed: 41 times | Downloaded: 8 times

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Original Uploader

Workflow get human and mouse phenotypes for a gene (2)

Created: 20/05/11 @ 15:18:50 | Last updated: 29/03/12 @ 09:01:06

Credits: User Tim Beck

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow gets phenotype annotations associated with human genes and the mouse orthologs from human (GWAS Central) and mouse (EuroPhenome and MGI) databases.

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

Viewed: 69 times | Downloaded: 14 times

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Packs (2)
Creator

Pack Towards Genotype-Phenotype Correlations


Created: 08/04/09 @ 13:14:54 | Last updated: 11/08/09 @ 14:50:01

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...

1 item in this pack

Comments: 0 | Viewed: 167 times | Downloaded: 38 times

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Creator

Pack Pathway to Phenotype using Text Mining


Created: 10/08/09 @ 13:01:47 | Last updated: 11/08/09 @ 14:51:31

This pack contains a list of workflows and result files obtained from the analysis of candidate pathways believed to play a role in resistance to African Trypanosomiasis in the mouse model organism.

0 items in this pack

Comments: 0 | Viewed: 200 times | Downloaded: 37 times

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