Difference between revisions of "Ky Roland"

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'''Significant Genes:''' <br>
 
'''Significant Genes:''' <br>
 
*'''Sphk2'''- [http://www.genecards.org/cgi-bin/carddisp.pl?gene=Sphk2 Gene Cards ] <br>
 
*'''Sphk2'''- [http://www.genecards.org/cgi-bin/carddisp.pl?gene=Sphk2 Gene Cards ] <br>
** 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 <br>
  
Ontological Discovery Environment ID- What GeneWeaver uses
+
Ontological Discovery Environment ID- What GeneWeaver uses <br>
*A common entity that gene species can map to in geneweaver
+
*A common entity that gene species can map to in geneweaver <br>
*to develop sets that you can match
+
*to develop sets that you can match<br>
  
 
Types of functional Genomics Data:
 
Types of functional Genomics Data:
  
Mapping Data
+
Mapping Data <br>
* QTL Positional Candidates
+
* QTL Positional Candidates <br>
*GWAS Candidate
+
*GWAS Candidate <br>
  
Expression Data: From NIF
+
Expression Data: From NIF <br>
*Drug Related Genes Database- from literature
+
*Drug Related Genes Database- from literature <br>
*Allen Brain Atlas- Mouse
+
*Allen Brain Atlas- Mouse <br>
** ensure localized expression
+
** ensure localized expression <br>
  
View similar gene sets
+
View similar gene sets <br>
Hierarchical similarity graph-  
+
Hierarchical similarity graph- <br>
*Top nodes are the most highly connected nodes, with the most highly connected gene being red
+
*Top nodes are the most highly connected nodes, with the most highly connected gene being red <br>
  
 
'''How to use GeneWeaver:''' <br>
 
'''How to use GeneWeaver:''' <br>
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HiSim- a sort of multiway venn diagram without overlapping results of high level intersections of gene sets <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
+
*Shows various combinations of intersecting gene sets <br>
*Emphasizes a relationship between the sets
+
*Emphasizes a relationship between the sets <br>
  
Gene Set Graph Tool  
+
Gene Set Graph Tool <br>
*Different way of looking at data comparisons made in HiSim, but more useful for emphasizing the genes
+
*Different way of looking at data comparisons made in HiSim, but more useful for emphasizing the genes <br>
 +
 
 +
Jacard Similarity- <br>
 +
View pairwise similarities and overlap <br>
 +
 
 +
 
 +
no method for two different score types- can upload gene sets twice using different score types and then threshold them in analysis <br>
 +
 
 +
Might have to convert Gene identifiers if they are mixed in the gene set <br>

Revision as of 15:49, 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

Jacard Similarity-
View pairwise similarities and overlap


no method for two different score types- can upload gene sets twice using different score types and then threshold them in analysis

Might have to convert Gene identifiers if they are mixed in the gene set