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Paul Fisher

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Pathway Abstracts for Day7 Microarray Tir1 QTL

Created: 2009-08-11 14:08:41 | Last updated: 2009-08-11 14:15:58

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This file contains all the abstracts for pathways found to be differentially expressed at day 7 post infection and intersect the Tir1 QTL region, from the African Trypanosomiasis project. Each pathway is listed as ">> [Pathway Name]", together with a PubMed identifier, date, and abstract for each article. Each pathway has been restricted to 500 abstracts, and is given in the date range 31/12/2007 to 01/01/2009. Note, some pathways do not have any abstracts available due to th...

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abstracts
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african trypanosomiasis
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authors
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cosine vector space
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data-driven
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enrichment
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esearch
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eutils
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genotype
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kegg
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Kegg Pathways
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pathway
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pathway-driven
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pathways
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phenotype
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pubmed
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term
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term extraction
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terms
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text
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text mining
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text mining; term extraction; entity recognition

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Paul Fisher

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Pathway Cosine Scores from Day7 and Tir1 QTL

Created: 2009-08-10 15:55:24

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This excel file contains a list of all pathways found to be differentially expressed at day 7 post infection in the trypanosomiasis resistance phenotype, which contain genes in the Tir1 QTL. The pathways in this file have been ranked according to the scores obtained after calculating a cosine vector value against the trypanosomiasis resistance phenotype. The higher the score, the more closely linked to a phentype a given pathway is. This allows each pathway to be ranked giving biologists a ...

File type: Excel workbook

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abstracts
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african trypanosomiasis
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cosine vector space
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data-driven
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kegg
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Kegg Pathways
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pathway
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pathway-driven
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pathways
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phenotype
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sleeping sickness
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term
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term extraction
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terms
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text
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text mining
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text mining; term extraction; entity recognition
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trait

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Paul Fisher

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Kegg pathways and genes

Created: 2009-04-08 19:26:26 | Last updated: 2009-08-10 11:41:55

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This file contains a list of all genes found within the Tir1 QTL region. These are represented as KEGG gene identifiers. Each gene is listed in tab deliminated format along with all KEGG pathway ids in which the gene is involved. These are given as KEGG pathway identifiers. Each gene may be included in zero or more pathways, with multiple instances of the same pathway being included in the file (due to multiple genes included in a single pathway).

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Paul Fisher

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Tir1 QTL - microarray day 7 intersecting pathways

Created: 2009-04-08 17:57:57

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This spreadhseet contains all of the intersecting pathways between the Tir1 QTL and day 7 differentially expressed genes

File type: Excel workbook

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Paul Fisher

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Candidate Gene protocol

Created: 2009-04-08 13:27:20

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This protocol provides details on how to identify candidate genes from the returned workflow results.

File type: Word document

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KNIME

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Pablo Carbonell

KNIME Workflow for RetroRules and Retropat... (3)

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KNIME Workflow for RetroRules and RetroPath2.0This worflow provides an examples of retrieving the RetroRules reaction rules for some given reaction identifiers.1. Input to the workflow: Chemical reactions expressed using public database identifiers.2. Each reaction queries RetroRules and outputs the corresponding reaction rules.3. Resulting list of rulesenzymes is stored in a csv file in RetroPath2.0 format.Installation notesThe workflow runs a Python scrpt that requires pandas: Python Data A...

Created: 2018-07-26 | Last updated: 2018-08-11

Credits: Pablo Carbonell

KNIME

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Pablo Carbonell

KNIME Workflow for RetroRules and Selenzyme (4)

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KNIME Workflow for RetroRules and SelenzymeThis worflow provides an examples of retrieving the RetroRules reaction rules for some given reaction and selecting enzyme sequences using the Selenzyme tool.1. Input to the workflow: Chemical reactions expressed using public database identifiers.2. Each reaction queries RetroRules and outputs the corresponding reaction rules.3. Each reaction rule queries Selenzyem and outputs the selected Uniprot sequences for each rule.4. Resulting list of selected...

Created: 2018-07-24 | Last updated: 2018-08-11

Credits: Pablo Carbonell

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Pablo Carbonell

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Pathway example for Selenzyme

Created: 2017-08-18 08:35:57 | Last updated: 2017-08-23 11:13:20

Credits: Pablo Carbonell

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Example of an input file containing information about a metabolic pathway to query the KNIME workflow for Selenzyme, an enzyme selection tool for pathway design.The file contains a list of reactions or generic reactions expressed in SMILES or SMARTS (SMIRKS) format. In the example, the list of reactions correspond to the different steps of a biosynthetic pathway.

File type: text/csv

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