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Category: Workflow Tag: gene

Workflow Render gene via BioGPS (1)

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This workflow uses the REST API of BioGPS to list the plugins and then allow the user to select which plugin to use to display the input gene id

Created: 2014-04-03

Credits: User Alex Nenadic

Workflow Find master regulators in networks (GeneWays) (1)

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This workflow is designed to find master regulatory molecules upstream of an input list of genes. Input file is any gene or protein table.At the first step, the input table is converted into a table with Entrez Gene IDs.At the next step the Entrez genes are annotated with additional information, gene description and gene symbols.The annotated gene table is subjected to master regulator search in the GeneWays network. For each potential master regulator, FDR, Score, and Z-score are calculated....

Created: 2013-11-13 | Last updated: 2015-04-17

Credits: User geneXplain

Workflow Mapping to ontologies (Gene table) (1)

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This workflow is designed to classify an input gene set to several ontologies and to identify terms, hits for which are overrepresented in the input set. The input file can be any gene or protein table.At the first step, the input table is converted into a table with Ensembl Gene IDs.This table with Ensembl Gene Ids is subjected to functional classification, which is done in parallel by the following ontologies: GO biological processes, GO cellular components, GO molecular functions, Reactome...

Created: 2013-11-13 | Last updated: 2015-04-17

Credits: User geneXplain

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Workflow Map genes to chromosomal location for T2WEB (1)

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This workflow maps a gene list on the genome using the biomart service. IMPORTANT NOTE: Keep in mind that for uploading files on t2web, you need to wait few minutes before executing the workflow. That's essential because the file needs first to be uploaded on the server.

Created: 2013-11-04

Credits: User Eleni

Uploader

Workflow get promoter region + operate on genomic i... (1)

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Finds the overlap between two datasets which contain genomic information (e.g. [gene id], chromosome name, gene start, gene end), plus some statistics. Returns rows of file_1 which overlap with the second file. A kolmogorov smirnov test is applied between the list that overlaps and the one that does not. NOTE: The library(GenomicRanges) is a prerequisite for this workflow

Created: 2013-11-04

Credits: User Eleni

Workflow Annotate a gene list with disease concepts (1)

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Purpose: Currently, this workflow takes a list of genes and a concept set as input, calculates the matching score between these and finds the concept that contributes the most to the match. Author comments: The workflow is in Beta stage. It runs, but needs more testing with different parameter settings. This workflow can be used together with other workflows in this pack: http://www.myexperiment.org/packs/368 for functional gene annotation and knowledge discovery.

Created: 2013-02-06

Credits: User Kristina Hettne User Reinout van Schouwen User Marco Roos Network-member BioSemantics

Attributions: Workflow SNPs to Concept Set through Concept Profile Matching v2

Workflow Match concept profiles with predefined set (2)

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Purpose of workflow: The workflow can be used to match a set of concept profiles with predefined set of concept profiles. Result: A list of concepts ordered by their match to the query concept profiles.

Created: 2013-02-05 | Last updated: 2014-07-14

Credits: User Kristina Hettne User Marco Roos User Reinout van Schouwen Network-member BioSemantics

Workflow Mining the Kegg pathway database with the ... (1)

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Genome-Wide Association studies (GWAS) with metabolomic phenotypes yield several statistically significant SNP-metabolite associations. To understand the biological basis of the association, scientists typically dwell on identifying genes in the vicinity of the SNP and the possible pathways that the gene participates in. The information needed to arrive at an understanding of the mechanistic basis of the association requires integration of disparate data sources. The purpose of this workflow ...

Created: 2013-01-30

Credits: User Marco Roos

Workflow ImportRefSeqtoKegg (3)

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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. This workflow uses the new KEGG REST service, which replaces the old SOAP interface from 31st December 2012

Created: 2012-11-12 | Last updated: 2013-01-08

Credits: User Katy Wolstencroft

Workflow Oryza Sativa QTLs and genes retrieval from... (2)

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For a given trait and QTL maximum size, retrieve accession numbers of the QTLs along with their mapping positions in Oryza sativa and retrieve genes present in the mapping genomic interval of a given QTL. Data integration from TropGene, Gramene and Ensembl relational databases. Semi-automatic creation of 7 Semantic Web Services for TropGene and Gramene with BioSemantic Use of BioMart Web Services for Ensembl interrogation

Created: 2012-08-08 | Last updated: 2012-09-28

Credits: User Julien wollbrett

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