Using this model, we derive a likelihood ratio test (LRT) that can simultaneously test for changes in mean expression (conditional on the gene being expressed) and in the percentage of expressed cells.
Conditional on the random effect, expression 4 corresponding to Weibull distribution in fact belongs to the family of parametric accelerated failure time (AFT) models [ 4].
Using these notations, we introduce the following model of single-cell expression (1) (2) (3) where denotes a point mass at zero, and are the -based mean and variance expression-level parameters conditional on the gene being expressed (i.e. ), and is the frequency of expression of gene across all cells.
In addition, the study design permitted QTL analysis conditional on gene expression, which led to the identification of loci whose genetic effects on the antibody response are causally linked through the eQTL.
We note that we used cMonkey to identify clusters of tumours conditional on common expression profiles across a set of genes, rather than the standard usage (to identify co-expressed genes across a subset of conditions), and therefore the data matrix was presented in a transposed form in comparison to normal usage.
In particular, we have applied biclustering to a large breast cancer expression data set that includes careful clinical annotations, and have used this method to identify clusters of breast tumours conditional on common expression profiles across a set of genes.
Under certain experimental conditions, the lifespan effects of ectopic dfoxo expression can be conditional on the nutrients available to the animal (Bai et al., 2012, Min et al., 2008).
The partial correlation Π jk here represents the conditional dependency between gene j and gene k, i.e, Π jk = 0 if the two genes are independent conditional on all other expression values and Π jk ≠ 0 if they are conditionally correlated.
However, the co-expression between two genes may be conditional on the phenotypic or biological context.
