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Exploring your Scatter Plot Insights

How to explore gene set and pathway enrichment insights from your scatter plot

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  1. Subset your data. In order to run an insight analysis on meaningful data points, filter your data from the data tab. Click on the arrow next to the column header of any property you would like to apply filters on. When working with a differential expression file, filters are commonly applied to the          P-Value and log2fold change. When filtering the data on the basis of the log2fold change it is best to run your insight analysis on genes that are upregulated and down-regulated separately. The threshold for what is considered upregulated and down-regulated is up to the discretion of the scientist.  We encourage you to try different filter stacks to determine what works best for your data.  Applying filters will subset your data and this will be reflected in your plot.
    1. An example of filters that can be applied to a differential expression file to analyze the pathway enrichments for upregulated genes would be Adjusted P Value < 0.05 and Log2FoldChange > 2.
    2. An example of filters that can be applied to a differential expression file to analyze pathway enrichments for down-regulated genes would be Adjusted P Value < 0.05 and  
      Log2FoldChange < -2. 
      Filter
  2. Once the filters have been applied in the data tab, head over to the "Insight" tab. The genes that satisfy the filter criteria you specified in Step 1 will be sent to EnrichR, KEGG, Reactome, and Gene Ontology for a gene set enrichment analysis.

    We break the insights down according to six different categories; 

    Category  Database/ Consortium 
    Pathways
    • Reactome
    • KEGG 
    Epigenetics
    • GeneSigDB
    • CORUM
    • Long non-coding RNA co-expression
    Ontology
    • Gene Ontology - Biological Process 
    • Gene Ontology - Molecular Function
    • Gene Ontology - Cellular Component
    Tissues/ Cells 
    • Cancer Cell Line Expression 
    Disease
    • MSigDB Computational 
    • ClinVar 2019
    Domains
    • InterPro Domains 2019
    • Pfam InterPro Domains
  3. Within all categories the insights from each database are displayed in a bar graph. To explore your      insights select a bar corresponding to a gene set or pathway. This will provide you with a list of all of the genes identified in your filtered data and the gene set or pathway you have selected. You will also be provided with a summary of the gene including the description, genomic coordinates, and biotype. Under the observations tab you will see all of the observations for each gene in all of the datasets you have uploaded or generated on the BioBox platform. 

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