Ky Roland

• 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