Difference between revisions of "Ky Roland"
From GcatWiki
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** Bears a relationship to Polr2a, another gene included in our list, but not significant | ** Bears a relationship to Polr2a, another gene included in our list, but not significant | ||
| − | + | Ontological Discovery Environment ID- What GeneWeaver uses | |
| + | *A common entity that gene species can map to in geneweaver | ||
| + | *to develop sets that you can match | ||
| + | |||
| + | Types of functional Genomics Data: | ||
| + | |||
| + | Mapping Data | ||
| + | * QTL Positional Candidates | ||
| + | *GWAS Candidate | ||
| + | |||
| + | Expression Data: From NIF | ||
| + | *Drug Related Genes Database- from literature | ||
| + | *Allen Brain Atlas- Mouse | ||
| + | ** ensure localized expression | ||
| + | |||
| + | View similar gene sets | ||
| + | Hierarchical similarity graph- | ||
| + | *Top nodes are the most highly connected nodes, with the most highly connected gene being red | ||
| + | |||
| + | '''How to use GeneWeaver:''' <br> | ||
| + | [http://www.beta.geneweaver.org GeneWeaver Beta] <br> | ||
| + | * Search a key term and data related to your search term will appear ranked by relevance <br> | ||
| + | *You can use boolean queries to augment your search results to be more or less inclusive<br> | ||
| + | |||
| + | HiSim- a sort of multiway venn diagram without overlapping results of high level intersections of gene sets <br> | ||
| + | *Shows various combinations of intersecting gene sets | ||
| + | *Emphasizes a relationship between the sets | ||
| + | |||
| + | Gene Set Graph Tool | ||
| + | *Different way of looking at data comparisons made in HiSim, but more useful for emphasizing the genes | ||
Revision as of 15:40, 15 February 2018
- 25 and 24 = paired reads, Male mouse 2078, C201R
23 and 22 = paired reads, Female mouse 2077, WT
21 and 20 = paired reads, Male mouse 2076, WT
19 and 18 = paired reads, Male mouse 2075, WT
17 and 16 = paired reads, Male mouse 2074, WT
- 15 and 14 = paired reads, Male mouse 2073, C201R
- 13 and 12 = paired reads, Female mouse 2072, C201R
- 11 and 10 = paired reads, Female mouse 2071, C201R
- 9 and 8 = paired reads, Female mouse 2070, C201R
7 and 6 = paired reads, Female mouse 2081, WT
5 and 4 = paired reads, Female mouse 2080, WT
- 3 and 2 = paired reads, Male mouse 2079, C201R
DESeq2- Comparison of WT vs. Mutant Females: Named-Types
- Mutant will be in numerator, and WT will be int he denominator; a number > 1 will mean that there is an overexertion in the wild type.
- We should not expect differential expression because the papers showed no significant differential mRNA expression between the mutant and wild type.
Significant Genes:
- Sphk2- Gene Cards
- Bears a relationship to Polr2a, another gene included in our list, but not significant
Ontological Discovery Environment ID- What GeneWeaver uses
- A common entity that gene species can map to in geneweaver
- to develop sets that you can match
Types of functional Genomics Data:
Mapping Data
- QTL Positional Candidates
- GWAS Candidate
Expression Data: From NIF
- Drug Related Genes Database- from literature
- Allen Brain Atlas- Mouse
- ensure localized expression
View similar gene sets Hierarchical similarity graph-
- Top nodes are the most highly connected nodes, with the most highly connected gene being red
How to use GeneWeaver:
GeneWeaver Beta
- Search a key term and data related to your search term will appear ranked by relevance
- You can use boolean queries to augment your search results to be more or less inclusive
HiSim- a sort of multiway venn diagram without overlapping results of high level intersections of gene sets
- Shows various combinations of intersecting gene sets
- Emphasizes a relationship between the sets
Gene Set Graph Tool
- Different way of looking at data comparisons made in HiSim, but more useful for emphasizing the genes
