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InviteGroup: PhD Supplementary Information
This group is only for examiners of my PhD thesis.
It contains all supplementary information listed in my thesis, and extra information in which to investigate all results a discussed with the thesis.
http://www.slideshare.net/fisherp/a-systematic-approach-to-genotypephenotype-correlations
Created at: Tuesday 11 August 2009 @ 14:41:06 (GMT)
Unique name: FisherpSupplementary
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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.
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Created: 11/08/09 @ 14:44:16 | Last updated: 11/08/09 @ 14:52:12
This pack is for investigating links between the genotype of an organisms to possible pathways. This constitutes half of the pathway-driven approach, genotype to pathway, and pathway to phenotype.
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Created: 05/07/10 @ 13:14:36 | Last updated: 26/01/11 @ 16:57:39
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This workflow takes in a list of gene names and searches the PubMed database for corresponding articles. Any matches to the genes are then retrieved (abstracts only). These abstracts are then returned to the user.
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Created: 05/07/10 @ 14:07:33 | Last updated: 11/01/11 @ 12:07:22
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This workflow takes in a phenotype search term, and searches for abstracts in the PubMed database. These are passed to the eSearch function and searched for in PubMed. Those abstracts found are returned to the user
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Created: 15/11/10 @ 12:08:18 | Last updated: 16/11/10 @ 16:07:49
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License: Creative Commons Attribution-Share Alike 3.0 Unported 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...
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Created: 15/11/10 @ 12:25:01 | Last updated: 15/11/10 @ 12:28:12
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
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.
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Created: 15/11/10 @ 12:30:21 | Last updated: 15/11/10 @ 12:30:59
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License: Creative Commons Attribution-Share Alike 3.0 Unported 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
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Created: 08/12/10 @ 11:35:18 | Last updated: 11/01/11 @ 12:05:41
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This workflow calculates the cosine vector space between two sets of corpora. The workflow then removes any null values from the output. this is some extra text vbeing added
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Created: 08/12/10 @ 11:38:37 | Last updated: 11/01/11 @ 12:02:30
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This workflow counts the number of articles in the pubmed database in which each term occurs, and identifies the total number of articles in the entire PubMed database. It also identified the total number of articles within pubmed so that a term enrichment score may be calculated. The workflow also takes in a document containing abstracts that are related to a particular phenotype. Scientiifc terms are then extracted from this text and given a weighting according to the number of terms that ...
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Created: 08/12/10 @ 11:47:10 | Last updated: 11/01/11 @ 12:00:16
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License: Creative Commons Attribution-Share Alike 3.0 Unported 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.
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Created: 08/12/10 @ 11:50:01 | Last updated: 11/01/11 @ 11:58:09
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This workflow takes in a document containg text and removes and non-ascii characters. The cleaned text is then sent to a service in dresden to extract all scientific terms. These terms represent a profile for the input document. Any null values are also removed.
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Created: 08/12/10 @ 11:55:03 | Last updated: 01/02/11 @ 11:33:11
This pack contains workflows to navigate from candidate Quantitative Trait genes and pathways to a given phenotype.
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