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Items tagged with "gene" (58)

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Files (11)
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Blob Candidate Gene protocol

Created: 08/04/09 @ 13:27:20

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This protocol provides details on how to identify candidate genes from the returned workflow results.

File type: Word document

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Blob Re-sequenced Daxx gene info

Created: 08/04/09 @ 17:53:46 | Last updated: 10/08/09 @ 12:30:59

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This spreadsheet contains information about the re-sequencing of the daxx gene, identified as a candidate QTg for the African Trypanosomiasis resiatance phenotype. This file is related to the paper: http://www.ncbi.nlm.nih.gov/pubmed/17709344

File type: Excel workbook

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Blob Tir1 QTL - Day 3 Microarray intersecting pathways

Created: 08/04/09 @ 17:56:10

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This spreadhseet contains all of the intersecting pathways between the Tir1 QTL and day 3 differentially expressed genes

File type: Excel workbook

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Blob Tir1 QTL - microarray day 7 intersecting pathways

Created: 08/04/09 @ 17:57:57

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This spreadhseet contains all of the intersecting pathways between the Tir1 QTL and day 7 differentially expressed genes

File type: Excel workbook

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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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Blob Kegg gene descriptions

Created: 08/04/09 @ 18:06:23 | Last updated: 10/08/09 @ 12:10:07

Credits: User 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

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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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Blob Gene Cosine Scores

Created: 10/08/09 @ 16:00:45

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This excel file contains a list of genes linked to the resistance to African trypanosomiasis in the mouse. Genes from the Tir1 QTL were used in a search through PubMed. The results were then correlated to the trypanosomiasis resistance phenotype. The higher the score (and ranking) the more related to the phenotype the gene is likely to be. This is based on the co-occurrence of terms within the gene and phentoype corpora.

File type: Excel workbook

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Blob Phenotype Concept Profile - Terms

Created: 11/08/09 @ 13:05:07 | Last updated: 11/08/09 @ 13:06:51

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This file contains a list of all terms extracted from the phenotype corpus, relating to African trypanosomiasis resistance in the mouse model. These terms were extracted using the following service: http://gopubmed4.biotec.tu-dresden.de/GoPubMedTermGenerationService/services/GoPubMedTermGeneration?wsdl These terms represent the concept profile for the phenotype.

File type: Plain text

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Blob Bilateral Perisylvian Polymicrogyria

Created: 17/03/11 @ 10:56:15 | Last updated: 17/03/11 @ 11:16:53

Credits: User Paul Fisher

Attributions: Workflow Pathway and Gene to Pubmed Workflow Pathways and Gene annotations forQTL region

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This zip file contains the results of running a QTL workflow for Bilateral Perisylvian Polymicrogyria in human (homo sapiens). Provided are a list of candidate QTL genes (QTg) and their corresponding KEGG pathways. Each gene and pathway have been subsequently run through a series of text mining workflows to determine the significance each may play in relation to Bilateral Perisylvian Polymicrogyria. If you want to help me identify candidate genes for this disorder, please get i...

File type: ZIP archive

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Blob Human Probeset data from Affymetrix

Created: 01/04/11 @ 09:08:45 | Last updated: 01/04/11 @ 09:08:51

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This file contains a list or affymetrix probest identifiers for Human gene expression data 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)

File type: Plain text

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Workflows (43)
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Workflow Mouse Microarray Analysis (3)

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

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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

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Workflow Gene annotation pipeline for the Graves di... (2)

Created: 03/10/07 @ 18:36:09 | Last updated: 22/11/07 @ 16:03:15

Credits: User Katy Wolstencroft User Peter Li

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

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This is a revised workflow for the Graves disease scenario gene annotation pipeline used in the myGrid project. The workflow had to be re-written due to the loss of the services invoked in the original workflow.

Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 1 | Citations: 0

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Workflow Human Microarray Analysis (1)

Created: 08/02/08 @ 14:30:17 | Last updated: 03/12/09 @ 16:50:29

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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  

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Workflow Get Kegg Gene information (2)

Created: 26/01/09 @ 18:06:12 | Last updated: 14/12/09 @ 12:05:21

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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

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Workflow Pathways and Gene annotations for Arabidop... (2)

Created: 06/03/09 @ 17:18:13 | Last updated: 03/12/09 @ 16:59:11

Credits: User Paul Fisher User Peter Li

Attributions: Workflow Pathways and Gene annotations for QTL region

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

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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: 237 times | Downloaded: 1 time

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Workflow omim and pathways (2)

Created: 03/03/09 @ 13:17:27 | Last updated: 02/11/09 @ 10:13:38

Credits: User Katy Wolstencroft User Paul Fisher

Attributions: Workflow Get Kegg Gene information

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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: 105 times | Downloaded: 41 times

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Original Uploader

Workflow NCBI Gi to Kegg Pathways (1)

Created: 08/06/09 @ 18:39:38 | Last updated: 14/12/09 @ 11:51:20

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow converts a list of NCBI gi numbers and  converts them to a list of KEGG genes. Those KEGG gene ids are subsequently turned into KEGG pathway identifiers and descriptions. It also removes any null values from a list of strings. Example input for this workflow is as follows (new line separated): gi:215422388 gi:120407068

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Workflow Cosine vector space (1)

Created: 10/08/09 @ 13:19:36 | Last updated: 10/08/09 @ 13:24:28

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow calculates the cosine vector space between two sets of corpora. The workflow then removes any null values from the output. The result is a cosine vector score between 0 and 1, showing the significance of any links between one concept (e.g. pathway) to another (e.g. phenotype). A score of 0 means there is no or an undetermined correlation between the two concepts. A score approaching 1 represents positive correlation.

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

Viewed: 62 times | Downloaded: 0 times

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Workflow Extract Scientific Terms (1)

Created: 10/08/09 @ 13:31:07 | Last updated: 10/08/09 @ 13:32:21

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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.

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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.

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Viewed: 163 times | Downloaded: 35 times

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Workflow Tab Parser (1)

Created: 19/08/09 @ 16:05:20

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow takes in a tab separated file, and then parses specific rows and columns from the file into an Ondex Graph. Additional prarameters are provided, though these are optional: graphId Long the ID of the Graph (REQUIRED) input String the plugin input (REQUIRED) skip Integer How many rows to skip at begin of document (Optional). Default value is 22. fromCol Integer Index of concept parser id for from concept. Default value is 0. (REQUIRED) toCol Integer Index of concept par...

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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

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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 ...

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Workflow caArray data retrieving (1)

Created: 23/11/09 @ 18:09:47

Credits: User Wei Tan

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Query all the gene expression data in a caArray experiment. Returns a evenly divided gene expression data set with corresponding class information. They ca be later used as training and test data set in many classification algorithms.Query all the gene expression data in a caArray experiment. Returns a evenly divided gene expression data set with corresponding class information. They can be later used as training and test data set in many classification algorithms.

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Workflow Get Gene Ids for Human (1)

Created: 04/02/10 @ 12:47:16 | Last updated: 04/02/10 @ 12:48:11

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow gets a list of gene ids (number depending on Ret_Max_value variable) for Homo sapiens. The species may be changed according to that desired, by altering the term_value string constant

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Workflow Kegg pathway diagrams (1)

Created: 13/03/10 @ 08:17:39

Credits: User Jannetta

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Find pathways in which all the genes in the list are involved. For each pathway draw the pathway diagram.for each protein draw a diagram of the Kegg pathway that its protein is involved in and where available visualise the structures

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Workflow Calculating frequencies of gene expression... (1)

Created: 15/03/10 @ 08:43:31

Credits: User Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow retrieves data from the MaxD microarray database and calculates the frequencies of gene expression levels using an R script

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Original Uploader

Workflow Entrez Gene to KEGG Pathway (2)

Created: 15/04/10 @ 12:22:12 | Last updated: 15/04/10 @ 12:22:13

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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

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Original Uploader

Workflow Get KEGG gene descriptions and pathways (1)

Created: 30/04/10 @ 16:09:29 | Last updated: 30/04/10 @ 16:12:02

Credits: User Nadia Cerezo User Paul Fisher

Attributions: Workflow Get Kegg Gene information

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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

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Workflow Gene to Pubmed (3)

Created: 05/07/10 @ 13:14:36 | Last updated: 26/01/11 @ 16:57:39

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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: 3 | Reviews: 0 | Comments: 0 | Citations: 0

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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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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

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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

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Workflow Pathway and Gene to Pubmed (2)

Created: 10/02/11 @ 16:10:52 | Last updated: 18/02/11 @ 13:47:08

Credits: User Paul Fisher

Attributions: Workflow Cosine vector space Workflow Extract Scientific Terms Workflow Rank Phenotype Terms Workflow Cosine vector space Workflow Rank Phenotype Terms Workflow Pathway to Pubmed Workflow Extract Scientific Terms Workflow Gene to Pubmed

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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

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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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Workflow gene subset extract (1)

Created: 29/03/11 @ 14:55:31 | Last updated: 29/03/11 @ 15:00:22

Credits: User Naser User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow functions for matching a set of genes as a part of whole gene data set and aim to extract the subset as a separate list.

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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

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Workflow tblastx non-redundant alignment (1)

Created: 30/06/11 @ 15:26:13 | Last updated: 04/07/11 @ 16:51:41

Credits: User Carol Lushbough

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow carries out alignments using TCoffee and ClustalW2 for a set of non-redundant proteins where the starting point is a particular genomic coding sequence representing only one member of the gene family in a given species.   For the BioExtract Server implementation, the necessary steps for accomplishing this task involve: 1.   Selecting the NCBI tblastx tool and providing the accession number of the known nucleotide sequence record as input. 2.   The output from ...

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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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Workflow Extract Gene Sequence with Kepler (1)

Created: 05/10/11 @ 05:04:40 | Last updated: 05/10/11 @ 05:04:42

Credits: User Wdsnellg

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This is a workflow which allows one to extract gene sequence information using the accession number as the input.  Multiple outputs include a file output of sequence header information, as well as one output window of base pair count, ratios and gene sequence.

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Workflow NCBI Gi to Kegg Pathway Descriptions (2)

Created: 12/01/12 @ 09:46:31 | Last updated: 12/01/12 @ 14:54:37

Credits: User Katy Wolstencroft

Attributions: Workflow NCBI Gi to Kegg Pathways

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow accepts a list of genbank gene identifiers and returns descriptions of gene functions and a list of all pathways each gene is involved in, according to the KEGG database.

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

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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

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Workflow Reactome pathways (1)

Created: 16/01/12 @ 15:31:40

Credits: User Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow returns a list of pathways gene products are involved in, along with their descriptions and Gene Ontology annotations

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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.

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Workflow Associated Region to Gene List (1)

Created: 08/02/12 @ 16:14:17 | Last updated: 08/02/12 @ 16:14:47

Credits: User Paul martin

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Produces a gene list from the Associated Region XML file

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Workflow Get Pathway-Genes by Entrez gene id (4)

Created: 08/03/12 @ 11:47:39 | Last updated: 14/04/12 @ 15:14:49

Credits: User Eleni

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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

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Workflow Get Pathway-Genes and gene description by ... (2)

Created: 27/03/12 @ 10:52:31 | Last updated: 03/04/12 @ 09:20:02

Credits: User Eleni

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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: 28 times | Downloaded: 11 times

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Workflow DatabaseID_to_ConceptID (4)

Created: 25/06/12 @ 20:48:28 | Last updated: 14/09/12 @ 10:03:01

Credits: User Marco Roos User Martijn Schuemie User Reinout van Schouwen Network-member BioSemantics

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Purpose: This workflow maps input Identifiers, common database identifiers, to the Concept Identifiers from the EMC ontology. Result: Concept Identifiers from the EMC ontology. Resources: Table of database identifiers and concept identifiers. Database identifiers from ... EMC ontology compiled from ... Comments: 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.

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

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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.

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

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Workflow Match concept profiles (4)

Created: 02/12/11 @ 09:07:34 | Last updated: 14/09/12 @ 09:57:48

Credits: User Marco Roos User Kristina Hettne User Martijn Schuemie User Reinout van Schouwen

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Purpose of workflow: The workflow can be used to match a set of concept profiles with another set of concept profiles. The result is a list of concepts ordered by their match to the query concept profiles. The workflow matches two sets of concept profiles. At the time of writing the concepts are derived from human, rat, and mouse terminologies, ontologies, and database identifiers. The profiles are lists of concepts ranked by their association with the identifying concept, as determined by c...

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

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Workflow SNPs to Concept Set through Concept Profil... (5)

Created: 26/06/12 @ 10:27:33 | Last updated: 14/09/12 @ 10:10:23

Credits: User Kristina Hettne User Eleni User Harish Dharuri User Reinout van Schouwen User Marco Roos User Martijn Schuemie Network-member BioSemantics

Attributions: Workflow Find Supporting Documents Workflow SNP_ID2EntrezGene_ID Workflow DatabaseID_to_ConceptID Workflow Match gene lists based on information in literature Workflow Match concept profiles Workflow Explain concept scores

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Purpose: Currently, this workflow takes one SNP and a concept set as input, calculates the matching score between these, finds co-occuring documents between the query concept and the match concept, finds the concept that contributes the most to the match, and the documents that support this finding. 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...

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

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

Created: 08/08/12 @ 14:34:48 | Last updated: 28/09/12 @ 15:02:53

Credits: User Julien wollbrett

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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

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

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Packs (4)
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Pack 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.

0 items in this pack

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Pack Extract Gene Sequence Information with Kepler


Created: 05/10/11 @ 04:58:33 | Last updated: 05/10/11 @ 06:11:56

This workflow and pack were designed for a class project.  The Kepler based workflow allows one to extract specific information from a gene sequence by using the accession ID as input.  By using two web services created for the DNA Data Bank of Japan (DDBJ, http://www.xml.nig.ac.jp/wabi/Method?serviceName=DDBJ&mode=methodList&lang=en), one can extract the sequence header information as an output file, as well as retrieve the sequence, base pair count, and base pair ratios in...

4 items in this pack

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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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