myExperiment - Tags

Workflows (20)

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: 1159 times \| Downloaded: 462 times Tags (9): entrez \| genotype \| kegg \| ncbi \| pathway \| pathway-driven \| pathways \| phenotype \| shim	View Download (v5)
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 Giovanni Dall'Olio	Basic eSearch/eFetch cycle (v1) Created: 04/12/08 @ 22:47:43 \| Last updated: 04/12/08 @ 22:51:42 Credits: Giovanni Dall'Olio License: Creative Commons Attribution-Share Alike 3.0 Unported License This is a basic eSearch/eFetch workflow created with taverna and using eUtils from NCBI. It accepts a query term as input (at the moment, for testing purposes, this is a fixed string), interrogate eSearch to retrieve the list of related sequences on the Nucleotide database, and use eFetch to retrieve the corresponding sequences. I wrote this workflow one year ago, when I was trying to understand how taverna and eUtils work; I suspect it broken, and of course it could be enhanced, so I am ... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 139 times \| Downloaded: 46 times Tags (6): efetch \| entrez \| esearch \| eutils \| example \| webenv	View Download (v1)
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
XProc Original Uploader Pierre Lindenbaum	Query dbsnp, transform to HTML (v1) Created: 21/05/09 @ 22:01:55 \| Last updated: 21/05/09 @ 23:12:33 Credits: Pierre Lindenbaum License: Creative Commons Attribution-Share Alike 3.0 Unported License This is a XProc worklow. Its input is a list of Entrez queries packed in a html list: See http://plindenbaum.blogspot.com/2009/05/xml-pipelines-xproc-for-bioinformatics.html "snp_gene_clin"[Filter] AND "snp_pubmed_cited"[Filter] AND 2[CHR] (1000[CHRPOS] : 5000[CHRPOS]) AND 2[CHR] AND "homo sapiens"[Organism] it queries entrez, download the SNPs as XML and transform the result as an HTML table: r... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 51 times \| Downloaded: 26 times Tags (7): dbsnp \| efetch \| entrez \| esearch \| snp \| xproc \| xslt	View Download (v1)
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	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 Paul Fisher	Phenotype to pubmed (v3) Created: 05/07/10 @ 14:07:33 \| Last updated: 11/01/11 @ 12:07:22 Credits: Paul Fisher License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow takes in a phenotype search term, and searches for abstracts in the PubMed database. These are passed to the eSearch function and searched for in PubMed. Those abstracts found are returned to the user Rating: 0.0 / 5 (0 ratings) \| Versions: 3 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 109 times \| Downloaded: 28 times Tags (18): abstracts \| african trypanosomiasis \| disease \| efetch \| entrez \| esearch \| loci \| ncbi \| phenotype \| pubmed \| qtl \| quanitative \| sleeping sickness \| term \| text \| text mining \| text mining; term extraction; entity recognition \| trait	View Download (v3)
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	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	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 Marco Roos	Gene expression interpretation by the Global Test (v1) Created: 26/04/11 @ 08:31:51 \| Last updated: 26/04/11 @ 08:31:52 Credits: Marco Roos License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow adds meaning to gene expresion values by performing a standard and a literature weighted Global Test. Gene expression is expected to be from Affymetrix microarrays, for which an RMA normalization and entrez Gene ID mapping/summation is performed. Original workflow is by Dennis Leenheer, edits by Marco Roos. Scripts by Kristina Hettne, acknowledging Rob Jellier, Jelle Goeman, and Peter-Bram 't Hoen. The workflow was created for the LUMC BioSemantics group, part of the Human Gen... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 29 times \| Downloaded: 0 times Tags (8): biosemantics \| e-science \| entrez \| gene expression \| GO \| normalization \| phenotype \| text_mining	View
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 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: 4932 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)
Bioclipse Scripting Language Original Uploader Egon Willighagen	Map a Entrez Gene ID to a Gene Ontology ID (v1) Created: 07/01/12 @ 10:01:05 Credits: Egon Willighagen License: MIT License BSL Groovy script that uses BridgeDB to convert a Entrez Gene identifier into a Gene ontology identifier. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 8 times \| Downloaded: 3 times Tags (5): bioclipse \| bridgedb \| entrez \| gene ontology \| groovy	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 (1)

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...

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Files (2)

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.

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Paul Fisher

Ensembl gene report

Created: 08/04/09 @ 19:30:15 | Last updated: 10/08/09 @ 11:05:59

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This file contains all genes identified in the Tir1 QTL region. Each gene is (if available) associated with an Entrez, UniProt, External Gene Id, Affymetrix probeset identifers (mouse_430_A chip), and Ensembl identifers for genes and their transcripts.

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Items tagged with "entrez" (23)