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Items tagged with "kegg" (58)

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Workflows (46)

Taverna 2 Original Uploader Paul Fisher	Pathways and Gene annotations for QTL region (v7) Created: 19/11/09 @ 18:18:52 \| Last updated: 02/09/11 @ 11:44:57 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 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: 4.9 / 5 (8 ratings) \| Versions: 7 \| Reviews: 1 \| Comments: 6 \| Citations: 1 Viewed: 4944 times \| Downloaded: 839 times Tags (22): adasd \| chromosome \| data-driven \| disease \| ensembl \| entrez \| gene \| genes \| genotype \| kegg \| mouse \| nbiconworkflows \| pathway \| pathway-driven \| pathways \| phenotype \| qtl \| shim \| subworkflow \| uniprot	View Download (v7)
Taverna 1 Original Uploader Paul Fisher	HUMAN Microarray CEL file to candidate pathways (v4) Created: 03/10/07 @ 18:35:55 \| Last updated: 26/11/09 @ 17:34:24 License: Creative Commons Attribution-No Derivative Works 3.0 Unported License 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 returned 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 ... Rating: 5.0 / 5 (2 ratings) \| Versions: 4 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 1314 times \| Downloaded: 372 times Tags (12): affymetrix \| cel \| file \| genotype \| kegg \| microarray \| nbiconworkflows \| pathway-driven \| pathways \| phenotype \| shim	View Download (v4)
Taverna 1 Original Uploader Paul Fisher	Entrez Gene to KEGG Pathway (v5) Created: 04/12/09 @ 16:04:38 \| Last updated: 30/11/10 @ 12:18:53 Credits: Paul Fisher License: Creative Commons Attribution 3.0 Unported License This workflow takes in Entrez gene ids then adds the string "ncbi-geneid:" to the start of each gene id. These gene ids are then cross-referenced to KEGG gene ids. Each KEGG gene id is then sent to the KEGG pathway database and its relevant pathways returned. Rating: 4.8 / 5 (4 ratings) \| Versions: 5 \| Reviews: 0 \| Comments: 2 \| Citations: 0 Viewed: 1162 times \| Downloaded: 463 times Tags (9): entrez \| genotype \| kegg \| ncbi \| pathway \| pathway-driven \| pathways \| phenotype \| shim	View Download (v5)
Taverna 1 Original Uploader Paul Fisher	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 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 Viewed: 286 times \| Downloaded: 129 times Tags (11): common \| data-driven \| disease \| genotype \| kegg \| microarray \| pathway \| pathway-driven \| pathways \| phenotype \| similarity	View Download (v3)
Taverna 1 Original Uploader Paul Fisher	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 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: 517 times \| Downloaded: 135 times Tags (18): affmetrix \| cel \| data-driven \| disease \| expression \| file \| gene \| genotype \| kegg \| microarray \| mouse \| nbiconworkflows \| pathway-driven \| phenotype \| RNA \| shim \| uniprot	View Download (v3)
Taverna 1 Original Uploader Sirisha Gollapudi	kegg_gene_to_swissprot_identifier (v1) Created: 27/11/07 @ 11:53:11 \| Last updated: 28/11/07 @ 12:58:38 Credits: Sirisha Gollapudi License: Creative Commons Attribution-Share Alike 3.0 Unported License Takes a KEGG gene identifier, e.g. sce:YAL038W (yeast pyruvate kinase) and converts to the corresponding Swissprot identifier. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 1 \| Citations: 0 Viewed: 117 times \| Downloaded: 49 times Tags (5): gene identifier \| kegg \| pathways \| swissprot \| uniprot	View Download (v1)
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 Paul Fisher	Microarray CEL file to candidate pathways (v2) Created: 08/02/08 @ 14:17:23 \| Last updated: 13/02/09 @ 11:29:52 Credits: Paul Fisher Saeedeh License: Creative Commons Attribution-Share Alike 3.0 Unported License 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: 272 times \| Downloaded: 5 times Tags (17): affymetrix \| cel \| data-driven \| ddbj \| disease \| entrez \| gene identifier \| genotype \| kegg \| microarray \| mouse \| pathway \| pathway-driven \| pathways \| shim \| transcribe \| transcription	View
Taverna 1 Original Uploader Paul Fisher	Human Microarray Analysis (v1) Created: 08/02/08 @ 14:30:17 \| Last updated: 03/12/09 @ 16:50:29 Credits: Paul Fisher License: Creative Commons Attribution-Share Alike 3.0 Unported License 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 Viewed: 276 times \| Downloaded: 4 times Tags (17): affymetrix \| cel \| data-driven \| disease \| expression \| gene \| gene identifier \| genotype \| kegg \| microarray \| pathway \| pathway-driven \| pathways \| shim \| transcribe \| transcription \| uniprot	View
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 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 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 1 Original Uploader Rory	Kegg_DrugID (v1) Created: 18/03/09 @ 14:49:02 \| Last updated: 18/03/09 @ 14:51:28 Credits: Rory License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow accepts looks up drug identifiers from KEGG given a pathway identifier. You can enter a pathway ID in the form path:map07026 Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 1 \| Citations: 0 Viewed: 64 times \| Downloaded: 33 times Tags (4): drug \| example \| kegg \| pathway	View Download (v1)
Taverna 2 Original Uploader Francois Belleau	Get the list of GeneID for all pathways of a specified taxon (v1) Created: 28/04/09 @ 07:48:40 Credits: Francois Belleau License: Creative Commons Attribution-Share Alike 3.0 Unported License No description Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 55 times \| Downloaded: 33 times Tags (6): bio2rdf \| broken \| demo \| hcls2009 \| kegg \| pathways	View Download (v1)
Taverna 2 Original Uploader Francois Belleau	Insert in local triplestore GeneID and KEGG pathway (v1) Created: 28/04/09 @ 07:55:10 Credits: Francois Belleau License: Creative Commons Attribution-Share Alike 3.0 Unported License No description Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 54 times \| Downloaded: 30 times Tags (7): bio2rdf \| demo \| hcls2009 \| kegg \| pathway \| pathways \| triplestore	View Download (v1)
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	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 QTL Analysis (v1) Created: 08/07/09 @ 16:26:13 \| Last updated: 14/12/09 @ 11:59:14 Credits: Paul Fisher License: Creative Commons Attribution-No Derivative Works 3.0 Unported License This workflow searches for genes which reside in a QTL (Quantitative Trait Loci) region in Arabidopsis thaliana. 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 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: 63 times \| Downloaded: 30 times Tags (15): arabidopsis \| chromosome \| crop \| ensembl \| kegg \| loci \| locus \| nucleotide \| pathway \| pathways \| plants \| qtl \| thaliana \| trait \| uniprot	View Download (v1)
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 Francois Belleau	What is [query] from NCBI, EBI, UniProt and KEGG ? (v2) Created: 03/11/09 @ 04:29:15 \| Last updated: 03/11/09 @ 04:29:19 Credits: Francois Belleau License: Creative Commons Attribution-Share Alike 3.0 Unported License test values: query = paget disease query = pdb4 query = hk1 query = h1n1 This rdfiser query those four federated search services EB-Eye, KEGG LinkDB, NCBI Entrez and UniProt knowledgebase. RDF triples are returned for search statistics with Bio2RDF normalised URIs. This workflow should be used responsibly because it can generate high load at the provider resources. test values: query = paget disease query = pdb4 query = hk1 query = h1n1 query = paget disease query = pdb4 query = hk1 que... Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 125 times \| Downloaded: 28 times Tags (8): bio2rdf \| cognoscope \| eb-eye \| kegg \| ncbi \| rdfiser \| search \| uniprot	View Download (v2)
Taverna 2 Original Uploader Francois Belleau	Triplify KEGG database list [myexperiments:kegg_namespace2rdf] (v2) Created: 28/11/09 @ 18:06:16 \| Last updated: 30/11/09 @ 20:17:03 Credits: Francois Belleau License: Creative Commons Attribution-Share Alike 3.0 Unported License TAG: knowledgescope, kegg, bio2rdf, banff_manifesto, rdf Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 22 times \| Downloaded: 15 times Tags (5): banff_manifesto \| bio2rdf \| cognoscope \| kegg \| rdf	View Download (v2)
Taverna 2 Original Uploader Francois Belleau	Triplify search results from all KEGG databases [myexperiments:kegg_search_all2rdf] (v3) Created: 30/11/09 @ 20:44:13 \| Last updated: 30/11/09 @ 20:44:55 Credits: Francois Belleau License: Creative Commons Attribution-Share Alike 3.0 Unported License Search all KEGG databases using bfind SOAP service and merge results into a bmuri list and a ntriples string. Rating: 0.0 / 5 (0 ratings) \| Versions: 3 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 37 times \| Downloaded: 21 times Tags (6): bfind \| bio2rdf \| cognoscope \| kegg \| rdf \| search_all	View Download (v3)
Taverna 2 Original Uploader Francois Belleau	Triplify namespace list from global search services from EBI, KEGG, NCBI and UniProt [myexperiment:search_services_namespace2rdf] (v1) Created: 30/11/09 @ 21:38:23 \| Last updated: 30/11/09 @ 21:44:57 Credits: Francois Belleau License: Creative Commons Attribution-Share Alike 3.0 Unported License No description Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 22 times \| Downloaded: 13 times Tags (7): banff_manifesto \| bio2rdf \| cognoscope \| ebi \| kegg \| ncbi \| uniprot	View Download (v1)
Taverna 2 Original Uploader Francois Belleau	Triplify search results from KEGG bfind SOAP service [myexperiments:kegg_search2rdf] (v3) Created: 30/11/09 @ 16:21:05 \| Last updated: 30/11/09 @ 20:48:50 Credits: Francois Belleau License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow use KEGG's SOAP service provided to do a BFIND serch within one of the KEGG's official database. The results are returned in RDF ntriples format. Rating: 0.0 / 5 (0 ratings) \| Versions: 3 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 20 times \| Downloaded: 22 times Tags (6): bfind \| bio2rdf \| cognoscope \| kegg \| search \| soap	View Download (v3)
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 Paul Fisher	microRNA to KEGG Pathways and Abstracts (v1) Created: 17/03/10 @ 10:53:02 Credits: Paul Fisher Attributions: Pathways and Gene annotations for QTL region License: Creative Commons Attribution-Share Alike 3.0 Unported License Workflow takes in a text file of microRNAs from microCOSM (at the EBI) and outputs a list of KEGG pathway information, including genes in pathways and pathway abstracts from PubMed. The results can then be used in various text mining applications/workflows to rank the results against a given disease.Workflow takes in a file of microRNAs Rating: 5.0 / 5 (1 rating) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 150 times \| Downloaded: 2 times Tags (21): bconv \| beanshell \| elico \| ensembl \| esearch \| eutils \| gene identifier \| geneid \| genes \| homo sapiens \| kegg \| KeggID \| microrna \| ncbi \| pathway \| pathway-driven \| pathways \| pubmed \| swissprot \| text mining \| uniprot	View
Taverna 2 Original Uploader Andrew David King	KEGG Pathway Analysis (v1) Created: 19/03/10 @ 13:46:37 Credits: Baywatch Solutions License: Creative Commons Attribution-No Derivative Works 3.0 Unported License The KEGG pathway analysis of the workflow takes a list of UniProt accession numbers in any of the following formats with the following prefixes: External database Database prefix ----------------- --------------- NCBI GI ncbi-gi: NCBI GeneID ncbi-geneid: GenBank genbank: UniGene unigene: UniProt uniprot: It performs this using the web service bconv, provided by the KEGG database (Kanehisa et a... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 73 times \| Downloaded: 44 times Tags (1): kegg	View Download (v1)
Taverna 2 Original Uploader Ian Laycock	NCBI Gi to Kegg Pathways (v1) Created: 19/03/10 @ 13:47:39 \| Last updated: 19/03/10 @ 13:52:45 Credits: Ian Laycock nclteamc Attributions: color_pathway_by_objects NCBI Gi to Kegg Pathways License: Creative Commons Attribution-Share Alike 3.0 Unported License User inputs background and foreground colour to be used to highlight proteins in KEGG pathway image. User provides NCBI GI numbers. Worflow calculates KEGG ID and pathway ID and sends value to colour service, which adds colour to that KEGG id on pathway image. Also outputs kegg description, pathway description and url of image. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 84 times \| Downloaded: 32 times Tags (5): bconv \| color \| kegg \| ncbi \| pathway	View Download (v1)
Taverna 2 Original Uploader Ian Laycock	Compare genome, extract proteins which are drug targets, apply to KEGG pathway (v1) Created: 19/03/10 @ 13:16:24 \| Last updated: 19/03/10 @ 13:33:53 Credits: Ian Laycock nclteamc Attributions: fetchEnsemblSeqsAndBlast NCBI Gi to Kegg Pathways color_pathway_by_objects License: Creative Commons Attribution-Share Alike 3.0 Unported License Takes GI number for source (non-pathogenic) and target (pathogneic) genomes, extracts list of all proteins from each genome using GenBank database. Outputs prtoeins in FastA format. Creates database from source proteins using formatdb (locally installed) and blasts (local installed) proteins from target against this database. Extracts protens which are unique (no blast hits) to the target (pathogenic) genome based on eValue set by user. Takes unique proteins from target and blasts aga... Rating: 4.0 / 5 (1 rating) \| Versions: 1 \| Reviews: 0 \| Comments: 1 \| Citations: 0 Viewed: 150 times \| Downloaded: 58 times Tags (7): colour \| FASTA \| gi \| kegg \| pathway \| proteins \| sequence	View Download (v1)
Taverna 2 Original Uploader Paul Fisher	Entrez Gene to KEGG Pathway (v2) Created: 15/04/10 @ 12:22:12 \| Last updated: 15/04/10 @ 12:22:13 Credits: Paul Fisher License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow takes in Entrez gene ids then adds the string "ncbi-geneid:" to the start of each gene id. These gene ids are then cross-referenced to KEGG gene ids. Each KEGG gene id is then sent to the KEGG pathway database and its relevant pathways returned. Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 68 times \| Downloaded: 1 time Tags (7): entrez \| gene \| gene pattern \| geneid \| kegg \| pathway \| pathways	View
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 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	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 (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 Dennis Leenheer	[untitled] (v1) Created: 26/04/11 @ 14:50:37 \| Last updated: 26/04/11 @ 15:04:28 Credits: Dennis Leenheer License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow allows the user to search for processes that are involved with a certain gene. Using microarray-files (CEL-files), consisting of wild type and KO mice to which a stimulant is induced, the user can get an idea of the processes involved. (This is done using the global test and the literature weighted global test.) The results are then given as a text-file. Warning: workflow is not working (needs some revisions), all input is currently hardcoded! (You will have to change the file... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 15 times \| Downloaded: 9 times Tags (16): bioinformatics \| biosemantics \| datamining \| global test \| GO \| kegg \| literature weighted global test \| mapping \| normalization \| rma \| sommation \| taverna \| taverna 2 \| textmining \| weighted global test \| workflow	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)
Taverna 2 Original Uploader Eleni	Get Pathway-Genes by Entrez gene id (v4) Created: 08/03/12 @ 11:47:39 \| Last updated: 14/04/12 @ 15:14:49 Credits: Eleni License: Creative Commons Attribution-Share Alike 3.0 Unported License Given a specific entrez gene id, returns the pathways that this gene participates in and for each of those pathways which genes are associated with. The workflow outputs also a KEGG pathway map and the objects are colored according to the input color values. Rating: 0.0 / 5 (0 ratings) \| Versions: 4 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 32 times \| Downloaded: 15 times Tags (6): entrez \| gene \| id \| kegg \| pathway \| pathways	View Download (v4)
Taverna 2 Original Uploader Eleni	Get Pathway-Genes and gene description by Entrez gene id (v2) Created: 27/03/12 @ 10:52:31 \| Last updated: 03/04/12 @ 09:20:02 Credits: Eleni License: Creative Commons Attribution-Share Alike 3.0 Unported License Given a specific entrez gene id, returns the pathways that this gene participates in and for each of those pathways which genes (including their description) are associated with. Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 19 times \| Downloaded: 7 times Tags (7): entrez \| gene \| gene description \| id \| kegg \| pathway \| pathways	View Download (v2)

Packs (4)

Creator: Franck Tanoh	Example workflow for KEGG web service Created: 29/09/08 @ 13:28:02 \| Last updated: 08/10/08 @ 16:37:49 The pack contains a number of test workflows for kegg web service (and operations) 14 items in this pack Comments: 0 \| Viewed: 228 times \| Downloaded: 41 times Tags: kegg	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	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

Files (8)

Uploader: Paul Fisher	Kegg gene descriptions Created: 08/04/09 @ 18:06:23 \| Last updated: 10/08/09 @ 12:10:07 Credits: 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: 26 times \| Downloaded: 24 times Tags: gene \| kegg \| KeggID \| mouse	View Download
Uploader: Paul Fisher	Kegg-Uniprot-Entrez cross-references Created: 08/04/09 @ 19:23:53 \| Last updated: 10/08/09 @ 12:08:00 Credits: Paul Fisher License: Creative Commons Attribution-Share Alike 3.0 Unported License This file contains a list of KEGG gene identifiers, cross-referenced to UniProt and Entrez identifiers. The UniProt and Entrez ids were obtained from BioMart for genes located in the Tir1 QTL region. File type: Plain text Rating: 0.0 / 5 (0 ratings) \| Comments: 0 \| Viewed: 37 times \| Downloaded: 54 times Tags: entrez \| kegg \| KeggID \| uniprot	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	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 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	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	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