COT: an efficient and accurate method for detecting marker genes among many subtypes.

ABSTRACT:

Motivation

Ideally, a molecularly distinct subtype would be composed of molecular features that are expressed uniquely in the subtype of interest but in no others-so-called marker genes (MGs). MG plays a critical role in the characterization, classification or deconvolution of tissue or cell subtypes. We and others have recognized that the test statistics used by most methods do not exactly satisfy the MG definition and often identify inaccurate MG.

Results

We report an efficient and accurate data-driven method, formulated as a Cosine-based One-sample Test (COT) in scatter space, to detect MG among many subtypes using subtype expression profiles. Fundamentally different from existing approaches, the test statistic in COT precisely matches the mathematical definition of an id

SUBMITTER: Lu Y 

PROVIDER: S-EPMC9163574 | biostudies-literature | 2022

REPOSITORIES: biostudies-literature