myExperiment - Tags - Kegg Pathways

Workflows (24)

Taverna 1 Original Uploader Fong Chun Chan	DataBiNS - Data Mining Workflow for Biological Pathways and Non-Synonymous SNPs (v2) Created: 04/12/07 @ 23:43:01 \| Last updated: 04/12/07 @ 23:45:25 Credits: Fong Chun Chan License: Creative Commons Attribution-Share Alike 3.0 Unported License No description Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 435 times \| Downloaded: 128 times Tags (12): bioinformatics \| biomoby \| entrez \| hapmap \| kegg \| Kegg Pathways \| ls-snp \| OMIM \| pdb \| pubmed \| snps \| swiss prot	View Download (v2)
Taverna 1 Original Uploader Franck Tanoh	keggID to Kegg pathways with BioMoby services (v3) Created: 03/10/07 @ 18:36:22 \| Last updated: 05/03/08 @ 13:59:55 License: Creative Commons Attribution-No Derivative Works 3.0 Unported License This workflow retrieves KEGG pathway id and image given a KEGG gene id. e.g hsa:6402 or eco:b0002 Rating: 4.0 / 5 (1 rating) \| Versions: 3 \| Reviews: 0 \| Comments: 2 \| Citations: 0 Viewed: 265 times \| Downloaded: 121 times Tags (3): kegg \| Kegg Pathways \| KeggID	View Download (v3)
Taverna 1 Original Uploader Saeedeh	Escherichia coli : From cDNA Microarray Raw Data to Pathways and Published Abstracts (v1) Created: 08/05/08 @ 15:25:29 \| Last updated: 12/05/08 @ 09:01:37 Credits: Saeedeh Paul Fisher Attributions: HUMAN Microarray CEL file to candidate pathways License: Creative Commons Attribution-Share Alike 3.0 Unported License 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: 5.0 / 5 (1 rating) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 320 times \| Downloaded: 102 times Tags (6): e.coli \| kegg \| Kegg Pathways \| pathways \| pubmed \| systems biology	View Download (v1)
Taverna 1 Original Uploader Paul Fisher	Get Kegg Gene information (v2) Created: 26/01/09 @ 18:06:12 \| Last updated: 14/12/09 @ 12:05:21 Credits: Paul Fisher License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow gets a series of information relating to a list of KEGG genes supplied to it. It also removes any null values from a list of strings. Example input for this workflow is given below (new line separated): mmu:13163 hsa:1616 Rating: 5.0 / 5 (1 rating) \| Versions: 2 \| Reviews: 0 \| Comments: 1 \| Citations: 0 Viewed: 314 times \| Downloaded: 116 times Tags (6): gene \| gene identifier \| information \| kegg \| Kegg Pathways \| KeggID	View Download (v2)
Taverna 1 Original Uploader Paul Fisher	Pathways and Gene annotations for Arabidopsis affy data (v2) Created: 06/03/09 @ 17:18:13 \| Last updated: 03/12/09 @ 16:59:11 Credits: Paul Fisher Peter Li Attributions: Pathways and Gene annotations for QTL region License: Creative Commons Attribution-No Derivative Works 3.0 Unported License This workflow searches for genes obtained from affy_ath1 affymetrix probeset identifiers. 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 pathway database. Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 224 times \| Downloaded: 1 time Tags (12): affymetrix \| arabidopsis \| binfo \| entrez \| gene \| kegg \| Kegg Pathways \| ncbi \| pathway \| pathways \| swissprot \| uniprot	View
Taverna 2 Original Uploader Paolo	KEGG Gene IDs to KEGG Pathways (v1) Created: 04/06/09 @ 18:41:36 \| Last updated: 07/01/10 @ 15:31:37 Credits: Paolo Attributions: Pathways and Gene annotations for QTL region License: Creative Commons Attribution-Share Alike 3.0 Unported License this is a simplified version of Paul's workflow (linked?) that is designed to be provenance-friendly Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 97 times \| Downloaded: 54 times Tags (3): kegg \| Kegg Pathways \| provenancetesting	View Download (v1)
Taverna 1 Original Uploader Paul Fisher	Cosine vector space (v1) Created: 10/08/09 @ 13:19:36 \| Last updated: 10/08/09 @ 13:24:28 Credits: Paul Fisher 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. The result is a cosine vector score between 0 and 1, showing the significance of any links between one concept (e.g. pathway) to another (e.g. phenotype). A score of 0 means there is no or an undetermined correlation between the two concepts. A score approaching 1 represents positive correlation. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 54 times \| Downloaded: 0 times Tags (14): abstracts \| cosine vector space \| gene \| information \| Kegg Pathways \| pathway \| phenotype \| pubmed \| qtl \| terms \| text \| text mining \| text mining; term extraction; entity recognition \| vector	View
Taverna 1 Original Uploader Paul Fisher	Extract Scientific Terms (v1) Created: 10/08/09 @ 13:31:07 \| Last updated: 10/08/09 @ 13:32:21 Credits: Paul Fisher License: Creative Commons Attribution-Share Alike 3.0 Unported License 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: 125 times \| Downloaded: 0 times Tags (18): abstracts \| authors \| data-driven \| entity recognition \| gene \| getconcepts \| kegg \| Kegg Pathways \| mining \| mouse \| pathway-driven \| pathways \| phenotype \| sleeping sickness \| term extraction \| text \| text mining \| text mining; term extraction; entity recognition	View
Taverna 1 Original Uploader Paul Fisher	Arabidopsis thaliana Microarray Analysis (v1) Created: 08/07/09 @ 16:28:34 Credits: Paul Fisher License: Creative Commons Attribution-No Derivative Works 3.0 Unported License This workflow searches for genes which are found to be differentially expressed in a microarray study using Arabidopsis thaliana. The workflow requires an input of a list of differentially expressed AffyMetrix Probeset identifiers. Data is then extracted from BioMart to annotate each of the genes. The 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 pathway database. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 145 times \| Downloaded: 30 times Tags (19): affmetrix \| affymetrix \| arabidopsis \| bconv \| data-driven \| ensembl \| gene \| gene expression \| geneid \| genes \| genotype \| kegg \| Kegg Pathways \| microarray \| pathway \| pathways \| phenotype \| thaliana \| uniprot	View Download (v1)
Taverna 1 Original Uploader Paul Fisher	KEGG Pasrer (v1) Created: 19/08/09 @ 16:03:07 Credits: Paul Fisher License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow parses a KEGG species database into an Ondex Graph graphId - the ID of the Graph. inputDir - the plugin input directory Species - Use this parameter to specify the species to be loaded from the kegg database. Default value is all. ParseSequences - KEGG species code. Default value is false (boolean) ImportOrthologFillers - Import Ortholog Pathway Fillers. Default value is false (boolean) Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 33 times \| Downloaded: 2 times Tags (7): kegg \| Kegg Pathways \| KeggID \| ondex \| ovtk \| oxl \| species	View
Taverna 1 Original Uploader Paul Fisher	Pathways and Gene annotations for QTL region (v2) Created: 20/11/09 @ 14:04:37 \| Last updated: 20/11/09 @ 14:04:39 Credits: Paul Fisher Attributions: Pathways and Gene annotations for QTL region 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 Pig, Sus scrofa. 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 pathway ... Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 134 times \| Downloaded: 21 times Tags (28): annotation \| binfo \| chromosome \| data integration \| data-driven \| ensembl \| entrez \| gene \| gene identifier \| geneid \| genes \| kegg \| Kegg Pathways \| KeggID \| loci \| locus \| merge \| pathway \| pathway-driven \| pathways \| pig \| qtl \| quanitative \| species \| sus scrofa \| swissprot \| trait \| uniprot	View Download (v2)
Taverna 2 Original Uploader Paul Fisher	Get Kegg Pathway information (v1) Created: 10/03/10 @ 17:15:47 \| Last updated: 10/03/10 @ 17:18:47 Credits: Paul Fisher License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow gets a series of information relating to a list of KEGG pathways supplied to it. It also removes any null values from a list of strings. Example input: path:mmu04010 path:mmu05014 Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 89 times \| Downloaded: 41 times Tags (6): genes \| kegg \| Kegg Pathways \| KeggID \| pathway \| pathways	View Download (v1)
Taverna 2 Original Uploader Nadia Cerezo	Get KEGG gene descriptions and pathways (v1) Created: 30/04/10 @ 16:09:29 \| Last updated: 30/04/10 @ 16:12:02 Credits: Nadia Cerezo Paul Fisher Attributions: Get Kegg Gene information License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow takes a list of KEGG gene identifiers and supplies descriptions associated to said genes + pathways including all genes and the descriptions associated to said pathways. The list_to_string local beanshell scripts merely transform a given list into a string of unique not-null elements separated by new lines (for batch btit use). Note that the input is a real taverna list : multiple values must be declared as multiple values instead of a single string value with distinct identif... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 393 times \| Downloaded: 25 times Tags (11): gene \| gene identifier \| genes \| information \| kegg \| Kegg Pathways \| KeggID \| pathway \| pathways \| taverna \| workflow	View Download (v1)
Taverna 1 Original Uploader Katy Wolstencroft	omim and pathways (v2) Created: 03/03/09 @ 13:17:27 \| Last updated: 02/11/09 @ 10:13:38 Credits: Katy Wolstencroft Paul Fisher Attributions: Get Kegg Gene information License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow searches OMIM for entries associated with a particular disease in OMIM, returns the IDs and maps them to Kegg Gene IDs. For each gene, it then gets the description and any corresponding pathways those genes are involved with Rating: 4.0 / 5 (1 rating) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 93 times \| Downloaded: 35 times Tags (9): bconv \| disease \| disease-associated genes \| gene \| genes \| kegg \| Kegg Pathways \| OMIM \| pathways	View Download (v2)
Taverna 2 Original Uploader Paul Fisher	Pathways and Gene annotations for QTL region (v1) Created: 15/11/10 @ 12:08:18 \| Last updated: 16/11/10 @ 16:07:49 Credits: Paul Fisher Attributions: Pathways and Gene annotations for QTL region 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... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 33 times \| Downloaded: 10 times Tags (33): african trypanosomiasis \| binfo \| chromosome \| common \| data-driven \| database \| disease \| ensembl \| entrez \| gene \| gene identifier \| geneid \| genes \| genomic \| genotype \| kegg \| Kegg Pathways \| KeggID \| loci \| locus \| mouse \| pathway \| pathway-driven \| pathways \| phenotype \| qtl \| quanitative \| region \| sleeping sickness \| species \| trait \| trichuris muris \| uniprot	View Download (v1)
Taverna 2 Original Uploader Paul Fisher	Pathways and Gene annotations for RefSeq ids (v1) Created: 15/11/10 @ 12:25:01 \| Last updated: 15/11/10 @ 12:28:12 Credits: Paul Fisher 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. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 72 times \| Downloaded: 35 times Tags (34): affmetrix \| affymetrix \| bconv \| binfo \| chromosome \| common \| data-driven \| database \| disease \| ensembl \| entrez \| expression \| gene \| gene expression \| gene identifier \| geneid \| genes \| genomic \| kegg \| Kegg Pathways \| KeggID \| microarray \| mouse \| pathway \| pathway-driven \| pathways \| phenotype \| species \| swissprot \| trait \| transcribe \| transcription \| trichuris muris \| uniprot	View Download (v1)
Taverna 2 Original Uploader Paul Fisher	KEGG pathways common to both QTL and microarray based investigations (v1) Created: 15/11/10 @ 12:30:21 \| Last updated: 15/11/10 @ 12:30:59 Credits: Paul Fisher 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 Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 21 times \| Downloaded: 15 times Tags (21): affmetrix \| affymetrix \| binfo \| chromosome \| common \| data-driven \| gene expression \| gene identifier \| geneid \| genotype \| kegg \| Kegg Pathways \| KeggID \| microarray \| pathway \| pathway-driven \| pathways \| phenotype \| qtl \| quanitative \| trait	View Download (v1)
Taverna 2 Original Uploader Paul Fisher	Pathway to Pubmed (v2) Created: 08/12/10 @ 11:47:10 \| Last updated: 11/01/11 @ 12:00:16 Credits: Paul Fisher 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. Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 36 times \| Downloaded: 19 times Tags (13): abstracts \| concept \| data-driven \| genotype \| Kegg Pathways \| KeggID \| pathway \| pathway-driven \| pathways \| phenotype \| text \| text mining \| text mining; term extraction; entity recognition	View Download (v2)
Taverna 2 Original Uploader Paul Fisher	Pathways and Gene annotations forQTL region (v1) Created: 21/01/11 @ 16:56:47 \| Last updated: 21/01/11 @ 16:58:50 Credits: Paul Fisher 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 Cow, Bos taurus. 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 pathway data... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 19 times \| Downloaded: 13 times Tags (22): african trypanosomiasis \| bos taurus \| cattle \| chromosome \| cow \| ensembl \| entrez \| gene \| genes \| genotype \| kegg \| Kegg Pathways \| KeggID \| pathway \| pathways \| phenotype \| qtl \| quanitative \| re-use \| region \| sleeping sickness \| uniprot	View Download (v1)
Taverna 2 Original Uploader Paul Fisher	Gene to Pubmed (v4) Created: 08/02/11 @ 13:04:06 \| Last updated: 10/02/11 @ 16:01:41 Credits: Paul Fisher Attributions: Cosine vector space Extract Scientific Terms Rank Phenotype Terms Cosine vector space Rank Phenotype Terms Pathway to Pubmed Extract Scientific Terms 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. Rating: 0.0 / 5 (0 ratings) \| Versions: 4 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 43 times \| Downloaded: 23 times Tags (30): abstracts \| cosine vector space \| data-driven \| disease \| enrichment \| entity recognition \| evidence \| kegg \| Kegg Pathways \| literature \| loci \| locus \| medline \| microarray \| mining \| pathway \| pathway-driven \| pathways \| phenotype \| pubmed \| qtl \| ranking \| re-use \| term \| term extraction \| terms \| text \| text mining \| text mining; term extraction; entity recognition \| trichuris muris	View Download (v4)
Taverna 2 Original Uploader Paul Fisher	Pathway and Gene to Pubmed (v2) Created: 10/02/11 @ 16:10:52 \| Last updated: 18/02/11 @ 13:47:08 Credits: Paul Fisher Attributions: Cosine vector space Extract Scientific Terms Rank Phenotype Terms Cosine vector space Rank Phenotype Terms Pathway to Pubmed Extract Scientific Terms Gene to Pubmed License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow takes in a list of gene names and KEGG pathway descriptions, and searches the PubMed database for corresponding articles. Any matches to the genes are then retrieved (abstracts only). These abstracts are then used to calculate a cosine vector space between two sets of corpora (gene and phenotype, or pathway and phenotype). The 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 PubMe... Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 64 times \| Downloaded: 19 times Tags (36): annotation \| concept \| concept profile \| controlled vocabulary \| cosine vector space \| data integration \| data-driven \| dresden \| efetch \| enrichment \| entity recognition \| esearch \| eutils \| gene \| gene identifier \| geneid \| genotype \| kegg \| Kegg Pathways \| KeggID \| literature \| loci \| locus \| medline \| mesh \| pathway \| pathway-driven \| pathways \| phenotype \| pubmed \| qtl \| quanitative \| text mining \| text mining; term extraction; entity recognition \| trait \| triat	View Download (v2)
Taverna 2 Original Uploader Paul Fisher	Pathways and Gene annotations forQTL region (v2) Created: 17/03/11 @ 11:10:28 \| Last updated: 30/08/11 @ 10:40:14 Credits: Paul Fisher Attributions: Pathways and Gene annotations for QTL region 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 Human, Homo sapiens. 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 pathway ... Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 25 times \| Downloaded: 14 times Tags (26): bilateral perisylvian polymicrogyria \| chromosome \| data integration \| data-driven \| database \| disease \| ensembl \| entrez \| epilepsy \| gene \| gene identifier \| geneid \| genes \| genomic \| genotype \| homo sapiens \| human \| Kegg Pathways \| KeggID \| pathway \| pathway-driven \| pathways \| phenotype \| qtl \| quanitative \| uniprot	View Download (v2)
Taverna 2 Original Uploader Paul Fisher	Pathways and Gene annotations forQTL region (v1) Created: 24/03/11 @ 15:14:48 \| Last updated: 24/03/11 @ 15:37:48 Credits: Paul Fisher License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow searches for genes found from a set of differentially expressed probestes, in Human, Homo sapiens. The workflow requires an input human affymetrix probeset identifiers. 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 pathway database. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 23 times \| Downloaded: 12 times Tags (12): data-driven \| entrez \| homo sapiens \| human \| kegg \| Kegg Pathways \| KeggID \| microarray \| pathway \| pathway-driven \| pathways \| uniprot	View Download (v1)
Taverna 2 Original Uploader Paul Fisher	Pathways and Gene annotations for QTL region (v1) Created: 27/05/11 @ 11:06:11 \| Last updated: 27/05/11 @ 11:06:52 Credits: Paul Fisher 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 rice, Oryza sativa. 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 UniGene 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 pathway d... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 30 times \| Downloaded: 9 times Tags (15): chromosome \| entrez \| genes \| genotype \| kegg \| Kegg Pathways \| loci \| locus \| pathway \| pathways \| phenotype \| qtl \| quanitative \| rice \| trait	View Download (v1)

Packs (6)

Creator: Paul Fisher	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... 20 items in this pack Comments: 0 \| Viewed: 159 times \| Downloaded: 34 times Tags: affymetrix \| african trypanosomiasis \| cattle \| data-driven \| disease \| entrez \| genotype \| Kegg Pathways \| KeggID \| link-integration \| microarray \| mouse \| pathway \| pathway-driven \| phenotype \| sleeping sickness \| swissprot \| uniprot \| web services	View Download
Creator: Paul Fisher	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. 12 items in this pack Comments: 0 \| Viewed: 190 times \| Downloaded: 34 times Tags: abstracts \| african trypanosomiasis \| authors \| beanshell \| data-driven \| daxx \| eutils \| information \| kegg \| Kegg Pathways \| mining \| mouse \| pathway \| pathway-driven \| pathways \| phenotype \| pubmed \| qtl \| sleeping sickness \| terms \| text \| text mining \| trait \| workflow	View Download
Creator: Paul Fisher	Genotype to Pathway 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. 18 items in this pack Comments: 0 \| Viewed: 88 times \| Downloaded: 7 times Tags: affmetrix \| affymetrix \| african trypanosomiasis \| bconv \| binfo \| chromosome \| common \| data-driven \| gene expression \| gene identifier \| geneid \| genes \| genotype \| Kegg Pathways \| KeggID \| loci \| locus \| pathway \| pathways \| qtl \| sleeping sickness \| swissprot	View Download
Creator: Paul Fisher	Text Mining Workflows 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. 5 items in this pack Comments: 0 \| Viewed: 77 times \| Downloaded: 12 times Tags: concept profile \| cosine vector space \| data-driven \| efetch \| entity recognition \| esearch \| gene \| gene identifier \| geneid \| genes \| genotype \| kegg \| Kegg Pathways \| KeggID \| literature \| loci \| locus \| ncbi \| pathway \| pathway-driven \| pathways \| phenotype \| pubmed \| qtl \| quanitative \| ranking \| space \| term \| term extraction \| terms \| text \| text mining \| text mining; term extraction; entity recognition \| trait \| vector	View Download
Creator: Paul Fisher	Trichuriasis induced Colitis Created: 16/02/11 @ 12:49:21 \| Last updated: 16/02/11 @ 15:26:36 This pack contains the workflows and data relating to Trichuriasis induced colitis. 5 items in this pack Comments: 0 \| Viewed: 16 times \| Downloaded: 2 times Tags: annotation \| chromosome \| controlled vocabulary \| cosine vector space \| data integration \| data-driven \| dresden \| efetch \| enrichment \| ensembl \| entity recognition \| esearch \| evidence \| gene expression \| gene identifier \| genotype \| kegg \| Kegg Pathways \| KeggID \| literature \| loci \| locus \| medline \| microarray \| mining \| pathway \| pathway-driven \| phenotype \| pubmed \| qtl \| quanitative \| ranking \| re-use \| significance \| term \| term extraction \| terms \| text \| text mining \| text mining; term extraction; entity recognition \| trait \| trichuris muris	View Download
Creator: Paul Fisher	Open Data: Bilateral Perisylvian Polymicrogyria Created: 16/11/10 @ 16:20:43 \| Last updated: 23/09/11 @ 10:55:08 This pack contains freely accessible data for scientific researchers to try and identify key genes linked to Bilateral Perisylvian Polymicrogyria. For those who want more information about this condition before they download the data, please see this link, which describes the condition and traits: http://omim.org/entry/300388?search=bilateral%20perisylvian%20polymicrogyria The results conatined within this pack are the output from running a scientific workflow that identifies candidate genes... 7 items in this pack Comments: 0 \| Viewed: 124 times \| Downloaded: 21 times Tags: bilateral perisylvian polymicrogyria \| bioinformatics \| chromosome \| cosine vector space \| data-driven \| epilepsy \| genotype \| homo sapiens \| human \| Kegg Pathways \| phenotype \| text mining; term extraction; entity recognition \| trait	View Download

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Mariebrown

metabolomics

Created: Thursday 29 November 2007 @ 11:50:47 (GMT)

Data analysis and bioinformatics of metabolomic studies

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Files (10)

Uploader: Paul Fisher	Candidate Gene protocol Created: 08/04/09 @ 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 Rating: 0.0 / 5 (0 ratings) \| Comments: 0 \| Viewed: 37 times \| Downloaded: 39 times Tags: affymetrix \| african trypanosomiasis \| gene \| gene identifier \| geneid \| Kegg Pathways \| KeggID \| pathway \| pathway-driven \| pathways \| phenotype \| sleeping sickness	View Download
Uploader: Paul Fisher	Kegg pathway identifiers Created: 08/04/09 @ 19:28:52 \| Last updated: 10/08/09 @ 11:03:00 Credits: Paul Fisher License: Creative Commons Attribution-Share Alike 3.0 Unported License This file contains a list of KEGG pathway identifiers, derived from a list of Ensembl genes found to be located with a given QTL/chromosomal region in the mouse. These genes are located in the Tir1 QTL. File type: Plain text Rating: 0.0 / 5 (0 ratings) \| Comments: 0 \| Viewed: 26 times \| Downloaded: 26 times Tags: kegg \| Kegg Pathways \| KeggID	View Download
Uploader: Paul Fisher	Kegg pathway descriptions Created: 08/04/09 @ 19:27:55 \| Last updated: 10/08/09 @ 11:29:34 Credits: Paul Fisher License: Creative Commons Attribution-Share Alike 3.0 Unported License This file contains a list of KEGG pathway descriptions, identified from genes found within the Tir1 QTL region (for African Trypanosomiasis). Each pathway may contain multiple genes from within the QTL region. File type: Plain text Rating: 0.0 / 5 (0 ratings) \| Comments: 0 \| Viewed: 18 times \| Downloaded: 18 times Tags: kegg \| Kegg Pathways \| KeggID	View Download
Uploader: Paul Fisher	Kegg pathways and genes Created: 08/04/09 @ 19:26:26 \| Last updated: 10/08/09 @ 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). File type: Plain text Rating: 0.0 / 5 (0 ratings) \| Comments: 0 \| Viewed: 22 times \| Downloaded: 22 times Tags: Kegg Pathways \| KeggID \| pathway \| pathway-driven \| pathways	View Download
Uploader: Paul Fisher	Kegg Pathway release Created: 08/04/09 @ 19:25:05 \| Last updated: 10/08/09 @ 12:06:18 Credits: Paul Fisher License: Creative Commons Attribution-Share Alike 3.0 Unported License This file contains the version of the KEGG pathway database used in the analysis of the Tir1 QTL region File type: Plain text Rating: 0.0 / 5 (0 ratings) \| Comments: 0 \| Viewed: 16 times \| Downloaded: 17 times Tags: database \| kegg \| Kegg Pathways	View Download
Uploader: Paul Fisher	Pathway Cosine Scores from Day7 and Tir1 QTL Created: 10/08/09 @ 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 Rating: 0.0 / 5 (0 ratings) \| Comments: 0 \| Viewed: 14 times \| Downloaded: 0 times Tags: abstracts \| african trypanosomiasis \| cosine vector space \| data-driven \| kegg \| Kegg Pathways \| pathway \| pathway-driven \| pathways \| phenotype \| sleeping sickness \| term \| term extraction \| terms \| text \| text mining \| text mining; term extraction; entity recognition \| trait	View
Uploader: Paul Fisher	Pathway Abstracts for Day7 Microarray Tir1 QTL Created: 11/08/09 @ 14:08:41 \| Last updated: 11/08/09 @ 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... File type: Plain text Rating: 0.0 / 5 (0 ratings) \| Comments: 0 \| Viewed: 16 times \| Downloaded: 0 times Tags: abstracts \| african trypanosomiasis \| authors \| cosine vector space \| data-driven \| enrichment \| esearch \| eutils \| genotype \| kegg \| Kegg Pathways \| pathway \| pathway-driven \| pathways \| phenotype \| pubmed \| term \| term extraction \| terms \| text \| text mining \| text mining; term extraction; entity recognition	View
Uploader: Paul Fisher	Trichuriasis Induced Colitis Created: 16/02/11 @ 15:16:17 \| Last updated: 16/02/11 @ 15:16:24 Credits: Paul Fisher Attributions: Pathways and Gene annotations for RefSeq ids KEGG pathways common to both QTL and microarray based investigations Pathways and Gene annotations for QTL region Pathway and Gene to Pubmed License: Creative Commons Attribution-Share Alike 3.0 Unported License This zip file contains the results of workflow runs for: identifying genes in each of the 7 QTL regions for Trichuris muris infection; identifying genes differentially expressed in mice challenged with Trichuris muris; and Text mining results (including cosine vector scores and Term Enrichment values). File type: Trident (Package) Rating: 0.0 / 5 (0 ratings) \| Comments: 0 \| Viewed: 8 times \| Downloaded: 6 times Tags: gene expression \| genotype \| Kegg Pathways \| microarray \| pathway-driven \| phenotype \| pubmed \| qtl \| trait \| trichuris muris	View Download
Uploader: Paul Fisher	Bilateral Perisylvian Polymicrogyria Created: 17/03/11 @ 10:56:15 \| Last updated: 17/03/11 @ 11:16:53 Credits: Paul Fisher Attributions: Pathway and Gene to Pubmed Pathways and Gene annotations forQTL region License: Creative Commons Attribution-Share Alike 3.0 Unported License This zip file contains the results of running a QTL workflow for Bilateral Perisylvian Polymicrogyria in human (homo sapiens). Provided are a list of candidate QTL genes (QTg) and their corresponding KEGG pathways. Each gene and pathway have been subsequently run through a series of text mining workflows to determine the significance each may play in relation to Bilateral Perisylvian Polymicrogyria. If you want to help me identify candidate genes for this disorder, please get i... File type: ZIP archive Rating: 0.0 / 5 (0 ratings) \| Comments: 0 \| Viewed: 12 times \| Downloaded: 7 times Tags: bilateral perisylvian polymicrogyria \| cosine vector space \| data integration \| data-driven \| enrichment \| entity recognition \| epilepsy \| gene \| homo sapiens \| human \| Kegg Pathways \| pathways \| phenotype \| pubmed \| qtl \| quanitative \| region \| text mining \| text mining; term extraction; entity recognition	View Download
Uploader: Paul Fisher	Human Gene expression data - Created: 01/04/11 @ 09:12:28 \| Last updated: 01/04/11 @ 09:12:40 Credits: Saeedeh Attributions: License: Creative Commons Attribution-Share Alike 3.0 Unported License This file contains a list processed for Human gene expression CEL files relating to the: Impact of NRSF variant over-expression in SK-N-AS human neuroblastoma cells (http://www.ebi.ac.uk/arrayexpress/browse.html?keywords=E-GEOD-22467&expandefo=on). The CEL files were analysed using the MADAT Taverna workflow available on myExperiment: http://www.myexperiment.org/workflows/2002.html File type: ZIP archive Rating: 0.0 / 5 (0 ratings) \| Comments: 0 \| Viewed: 7 times \| Downloaded: 5 times Tags: affmetrix \| affymetrix \| gene expression \| gene identifier \| homo sapiens \| human \| kegg \| Kegg Pathways \| madat \| pathway \| pathway-driven \| pathways \| r	View Download

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Items tagged with "Kegg Pathways" (41)