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Items tagged with "ensembl" (27)

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Files (2)
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Blob Ensembl database release

Created: 08/04/09 @ 18:00:35 | Last updated: 10/08/09 @ 12:12:09

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

The release of the Ensembl database used to identify genes in Tir1 QTL region.

File type: Plain text

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Uploader

Blob Ensembl gene report

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

Credits: User 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.

File type: Plain text

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Workflows (21)
Original Uploader

Workflow Mapping OligoNucleotides to an assembly (7)

Created: 13/02/09 @ 09:05:35 | Last updated: 13/02/09 @ 09:08:20

Credits: User Wassinki User Pieter Neerincx

Attributions: Workflow Blat against ENSEMBLE Danio_rerio_Genome Workflow BlatBlastCombi Workflow Blast against ENSEMBLE Danio_rerio_Genome Workflow AppendToFile Blob Test Input for Mapping oligonucleotides to an assembly Blob Input for Mapping oligonucleotides to an assembly

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Version info The former version of the workflow expected that results from BioMART only report transcripts when the query (the probe in our case) are entirely encapsulated in an exon of that transcript. However, the BioMart service also returns transcripts when the query is not or only partially overlapping with an exon in the stretch on the assembly on which a transcript is defined. This resulted in too many oligos classified as having multiple transcripts or having multiple genes. ...

Rating: 0.0 / 5 (0 ratings) | Versions: 7 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 627 times | Downloaded: 115 times

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Original Uploader

Workflow Biomart Protein Sequence Retrieval (1)

Created: 09/03/09 @ 11:38:10

Credits: User Kieren Lythgow

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow queries Biomart to retrieve the Ensembl gene id, protein id, gene name, description and amino acid sequence from the Ensembl Homo sapiens dataset. The user needs to specify a defined chromosomal region i.e. Chromo = 1, Start = 100000000, End = 250000000. This returns all unique entries in FASTA format.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 200 times | Downloaded: 48 times

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Original Uploader

Workflow Arabidopsis thaliana Microarray Analysis (1)

Created: 08/07/09 @ 16:28:34

Credits: User Paul Fisher

License: Creative Commons Attribution-No Derivative Works 3.0 Unported License

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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: 163 times | Downloaded: 35 times

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Original Uploader

Workflow Arabidopsis thaliana QTL Analysis (1)

Created: 08/07/09 @ 16:26:13 | Last updated: 14/12/09 @ 11:59:14

Credits: User Paul Fisher

License: Creative Commons Attribution-No Derivative Works 3.0 Unported License

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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. ...

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Original Uploader

Workflow chicken_ensembl_gene_id (1)

Created: 07/09/09 @ 15:00:01 | Last updated: 09/09/09 @ 14:21:48

Credits: User Rory

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Accepts a chromosome eg. 1 and returns the ensembl gene ids for that chromosome

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

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Original Uploader

Workflow Pathways and Gene annotations for QTL region (2)

Created: 20/11/09 @ 14:04:37 | Last updated: 20/11/09 @ 14:04:39

Credits: User Paul Fisher

Attributions: Workflow Pathways and Gene annotations for QTL region

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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: 142 times | Downloaded: 23 times

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Original Uploader

Workflow microRNA to KEGG Pathways and Abstracts (1)

Created: 17/03/10 @ 10:53:02

Credits: User Paul Fisher

Attributions: Workflow Pathways and Gene annotations for QTL region

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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: 163 times | Downloaded: 2 times

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Original Uploader

Workflow Pathways and Gene annotations for QTL region (1)

Created: 15/11/10 @ 12:08:18 | Last updated: 16/11/10 @ 16:07:49

Credits: User Paul Fisher

Attributions: Workflow Pathways and Gene annotations for QTL region

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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: 43 times | Downloaded: 14 times

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Original Uploader

Workflow Pathways and Gene annotations for RefSeq ids (1)

Created: 15/11/10 @ 12:25:01 | Last updated: 15/11/10 @ 12:28:12

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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: 85 times | Downloaded: 36 times

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Original Uploader

Workflow Pathways and Gene annotations forQTL region (1)

Created: 21/01/11 @ 16:56:47 | Last updated: 21/01/11 @ 16:58:50

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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: 30 times | Downloaded: 16 times

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Original Uploader

Workflow Pathways and Gene annotations forQTL region (2)

Created: 17/03/11 @ 11:10:28 | Last updated: 30/08/11 @ 10:40:14

Credits: User Paul Fisher

Attributions: Workflow Pathways and Gene annotations for QTL region

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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: 32 times | Downloaded: 16 times

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Original Uploader

Workflow BiomartAndEMBOSSDisease (4)

Created: 27/01/11 @ 17:03:03 | Last updated: 04/09/12 @ 09:32:08

Credits: User Katy Wolstencroft User Alan Williams

Attributions: Workflow BiomartAndEMBOSSAnalysis

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow retrieves all genes on human chromosome 22 that are associated with a disease and aligns the upstream regions with mouse and rat homologues. The alignments are plotted and corresponding sequence ids are also returned. Using Biomart and EMBOSS soaplab services, This workflow retrieves a number of sequences from 3 species: mouse, human, rat; align them, and returns a plot of the alignment result. Corresponding sequence ids are also returned.

Rating: 0.0 / 5 (0 ratings) | Versions: 4 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 131 times | Downloaded: 74 times

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Original Uploader

Workflow Pathways and Gene annotations for QTL region (7)

Created: 19/11/09 @ 18:18:52 | Last updated: 07/09/12 @ 18:23:36

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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: 4.6 / 5 (10 ratings) | Versions: 7 | Reviews: 1 | Comments: 7 | Citations: 1

Viewed: 6121 times | Downloaded: 1014 times

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Original Uploader

Workflow Biomart datasets for the Ensembl Genes mar... (1)

Created: 03/10/11 @ 10:17:40

Credits: User Rafael C. Jimenez

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Retrieve Biomart datasets for the Ensembl Genes mart service (one dataset per specie).

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 12 times | Downloaded: 10 times

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Original Uploader

Workflow Find Orthologs for proteins in Ensembl (1)

Created: 03/10/11 @ 14:33:04 | Last updated: 03/10/11 @ 14:33:07

Credits: User Rafael C. Jimenez

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Find Orthologs for proteins in Ensembl using biomart.

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Viewed: 15 times | Downloaded: 8 times

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Original Uploader

Workflow Find orthologs using a uniprot accession (1)

Created: 14/10/11 @ 13:07:41 | Last updated: 14/10/11 @ 13:07:44

Credits: User Rafael C. Jimenez

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Find orthologs based on ensembl information using as input/output uniprot accession

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

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Original Uploader

Workflow Find orthologs using a list of uniprot acc... (1)

Created: 14/10/11 @ 13:12:36 | Last updated: 14/10/11 @ 13:12:39

Credits: User Rafael C. Jimenez

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Find orthologs based on ensembl information using as input/output uniprot accessions

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Viewed: 12 times | Downloaded: 6 times

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Original Uploader

Workflow Import and convert gene list (1)

Created: 15/01/12 @ 10:23:33 | Last updated: 12/03/12 @ 11:59:15

Credits: User Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow extracts a column of RefSeq gene IDs from a CSV file and then converts them to Unigene identifiers

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 59 times | Downloaded: 103 times

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Original Uploader

Workflow Define Associated Regions and Genes (2)

Created: 08/02/12 @ 16:08:08 | Last updated: 09/05/12 @ 09:52:18

Credits: User Paul martin

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Defines regions and genes from associated SNPs A JAVA MySQL connector is required to run the workflow and must be placed in the $TAVERNA_HOME/lib directory.

Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0

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Original Uploader

Workflow SNP_ID2EntrezGene_ID (4)

Created: 26/06/12 @ 09:50:25 | Last updated: 14/09/12 @ 10:05:55

Credits: User Kristina Hettne User Harish Dharuri

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Purpose: The workflow maps a SNP (dbSNP id) to a gene (EntrezGene id). Author comments: The window for gene inclusion can be set using the set_width parameter. This workflow can be used together with other workflows in this pack: http://www.myexperiment.org/packs/282 for functional gene and SNP annotation and knowledge discovery.

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Original Uploader

Workflow ImportRefSeqtoKegg (1)

Created: 12/11/12 @ 14:31:05

Credits: User Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow extracts a column of RefSeq gene IDs from a CSV file and then converts them to Kegg gene identifiers

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 1 | Citations: 0

Viewed: 9 times | Downloaded: 1 time

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Packs (4)
Creator

Pack Package: mapping oligonucleotides to an assembly


Created: 11/12/08 @ 12:02:47 | Last updated: 22/01/09 @ 09:06:26

This package contains all elements required to run the RShell use case "Mapping oligonucleotides to an assembly"  

0 items in this pack

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Pack 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.

0 items in this pack

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Creator

Pack wf4ever Deliverable 6.3 Pack


Created: 02/12/11 @ 09:31:26 | Last updated: 02/12/11 @ 10:21:03

This pack contains (references to) the workflows for GWAS analysis by workflows that perform pathway and GO analysis and biosemantics data interpretation (a special form of text mining). This pack aggregates the deliverable materials for month 8 for Work Package 6. The workflows have not been published in the scientific domain yet, so its content cannot yet be made public. They are available upon request, in particular for reviewers. Please contact Kristina Hettne or Marco Roos (see credit...

2 items in this pack

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Pack Functional annotation of SNPs using next-generation ...


Created: 26/06/12 @ 10:41:38 | Last updated: 14/09/12 @ 10:53:41

This pack implements the concept profile matching pipeline in the knowledge discovery tool Anni (http://biosemantics.org/anni), and adapts it to interpret the top SNPs from a GWAS. The underlying literature and concept profile databases are the same as the for the current version of Anni (2.1). The pack consists of three main workflows (http://www.myexperiment.org/workflows/2999, http://www.myexperiment.org/workflows/2973, http://www.myexperiment.org/workflows/2972). Workflow 2999 returns a ...

0 items in this pack

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