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Items tagged with "qtl" (25)

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Files (5)
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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

Rating: 0.0 / 5 (0 ratings) | Comments: 0 | Viewed: 21 times | Downloaded: 22 times

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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

Rating: 0.0 / 5 (0 ratings) | Comments: 0 | Viewed: 27 times | Downloaded: 25 times

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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

Rating: 0.0 / 5 (0 ratings) | Comments: 0 | Viewed: 19 times | Downloaded: 16 times

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Blob Trichuriasis Induced Colitis

Created: 16/02/11 @ 15:16:17 | Last updated: 16/02/11 @ 15:16:24

Credits: User Paul Fisher

Attributions: Workflow Pathways and Gene annotations for RefSeq ids Workflow KEGG pathways common to both QTL and microarray based investigations Workflow Pathways and Gene annotations for QTL region Workflow Pathway and Gene to Pubmed

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This zip file contains the results of workflow runs for: identifying genes in each of the 7 QTL regions for Trichuris muris infection; identifying genes differentially expressed in mice challenged with Trichuris muris; and Text mining results (including cosine vector scores and Term Enrichment values).

File type: Trident (Package)

Rating: 0.0 / 5 (0 ratings) | Comments: 0 | Viewed: 9 times | Downloaded: 7 times

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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

Rating: 0.0 / 5 (0 ratings) | Comments: 0 | Viewed: 20 times | Downloaded: 8 times

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Workflows (16)
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 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. ...

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

Viewed: 70 times | Downloaded: 34 times

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Original Uploader

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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Original Uploader

Workflow Genomic Filter (1)

Created: 19/08/09 @ 16:19:01

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow filters a given Ondex graph according to a chromosomal region, or QTL region. The result is a new Ondex graph. The parameters that can be used with this service are as follows: graphId - the ID of the input Graph. outputGraphId - the ID of the output Graph (Optional). If no output graph is specified filtered items will be removed from the input graph. ContextID - The Concept ID of the Context (Chromosome). From - The start position on the chromosome, e.g. 100. To - The stop pos...

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

Viewed: 28 times | Downloaded: 1 time

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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

Tags (28):

Original Uploader

Workflow Phenotype to pubmed (3)

Created: 05/07/10 @ 14:07:33 | Last updated: 11/01/11 @ 12:07:22

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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: 130 times | Downloaded: 45 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

Tags (33):

Original Uploader

Workflow KEGG pathways common to both QTL and micro... (1)

Created: 15/11/10 @ 12:30:21 | Last updated: 15/11/10 @ 12:30:59

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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: 35 times | Downloaded: 17 times

Tags (21):

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

Tags (22):

Original Uploader

Workflow Rank Phenotype Terms (1)

Created: 01/02/11 @ 11:22:14 | Last updated: 01/02/11 @ 11:24:42

Credits: User Paul Fisher

Attributions: Workflow Cosine vector space Workflow Rank Phenotype Terms

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This 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 PubMed database. It also identified the total number of articles within pubmed so that a term enrichment score may be calculated. The workflow also takes in a document containing abstracts that are related to a particular phenotype. Scientiifc terms are then extracted from this text and given a weighting according to the number of terms that ...

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

Viewed: 34 times | Downloaded: 15 times

Tags (26):

Original Uploader

Workflow Gene to Pubmed (4)

Created: 08/02/11 @ 13:04:06 | Last updated: 10/02/11 @ 16:01:41

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

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: 4 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 51 times | Downloaded: 25 times

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Original Uploader

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

Viewed: 75 times | Downloaded: 20 times

Tags (36):

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

Tags (26):

Original Uploader

Workflow Pathways and Gene annotations for QTL region (1)

Created: 27/05/11 @ 11:06:11 | Last updated: 27/05/11 @ 11:06:52

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 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: 42 times | Downloaded: 12 times

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Original Uploader

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

Viewed: 33 times | Downloaded: 16 times

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Packs (4)
Creator

Pack 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.

0 items in this pack

Comments: 0 | Viewed: 200 times | Downloaded: 37 times

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Pack Genotype to Pathway


Created: 11/08/09 @ 14:44:16 | Last updated: 11/08/09 @ 14:52:12

This pack is for investigating links between the genotype of an organisms to possible pathways. This constitutes half of the pathway-driven approach, genotype to pathway, and pathway to phenotype.

0 items in this pack

Comments: 0 | Viewed: 97 times | Downloaded: 8 times

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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

Comments: 0 | Viewed: 86 times | Downloaded: 14 times

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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

Comments: 0 | Viewed: 22 times | Downloaded: 3 times

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