Basic statistics
Predicting interactions between genes
We used correlational analyses to predict genetic interactions. Jupyter Notebook
Transcriptome-wide epistasis analysis
Development of the formalism for, and measurement of, transcriptome-wide epistasis. Jupyter Notebook
Decorrelation within a pathway
Transcriptome weighted correlations between mutants decrease in magnitude the farther apart two genes are from each other. Jupyter Notebook
Non-canonical epistasis
Transcriptomes provide an unbiased view of genetic relationships, which can be used to identify epistasis relationships that are different from what is usually reported. Jupyter Notebook
Enrichment analysis of the hypoxia pathway
We use the WormBase Enrichment Suite to understand the biological functions that the hypoxia pathway is activating in C. elegans. Jupyter Notebook
Finding hif-1-independent responses
Our experimental design allows us to identify genes whose expression is hif-1-independent yet dependent on other genes. In other words, we identify branches in the pathway. Jupyter Notebook
Quality Check
There are known genes that have hif-1-dependent expression. Here, we check that these genes behave as expected from the literature. Jupyter Notebook
Contact us
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