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
  

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

Gene Weaver Tips:

• Use Gene ID's as the gene identifier
  

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Transcription Factors

Start with Gene search in NCBI.

Where is this expressed? (all 4 data sets)

Human conditions when mutated?

How many proteins does NR5A1 interact with?

What GO terms are associated with NR5A1?

nhr-25: Model Transcription Factor

• Background
  
  • an important developmental regulator
    
  • known phenotypes and tools
    
  • mammalian orthologs
    

• NHR-25
  
  • transcription factor of large family: nuclear hormone receptors
    
  • expressed in seam and vulval cells throughout development
    
  • human orthologs: SF-1 and LRH-1; and Drosophila: Ftz-F1
    

• Mutants to identify regulated genes
  
  • nhr-25 is essential, therefore we have to knockdown the gene as opposed to knocking it out
    
  • transiently knocked down by RNAi- molting and vulval defects
    

• • nhr-25(ku217) mutant- molting and vulval defect
    
    • leucine to proline point mutation in the D
      

NA biding domain

• • • mutant has reduced DNA binding
      

• identification of nhr-25 regulated genes
  
  • sequencing library consists of 10 worms from roughly the same developmental stage
    

Pairwise Comparisons:

• WT vs Mutant GOrilla
  
• WT vs. Knockdown GOrilla
  
• Mutant vs. Knockdown
  

Thought Process

• Narrow down list using adjusted p-value (cutoff of .01)
  
• Rank gene list based on fold change (largest to smallest)
  
• Input 3 ranked gene list into gene Venn
  
• Analyze list of genes from Gene Venn that show common genes from differential expression from all three DE comparisons
  
• Alanyze gene list of genes from Gene Venn that showgenes only expressed in WT vs. Mutant and not other 2 DE comparisons
  
  • Highest enrich
• Knockdown- point mutation, mRNA is still in tact
  
• RNAi- binds to mRNA and mRNA is destroyed; no protein is created
  
• Compare genes expressed in up regulated vs. down regulated genes and do GOrilla and WormBase analysis

• Vulva and cuticle are two phenotypes that we know are affected (known phenotypes) in the mutant and knockdown worms
  
• Wormbase limitation, it is comparing larger categories
  

Venn Diagram tool: Gene venn