Digging deep into Golgi phenotypic diversity with unsupervised machine learning

Abstract

Structural alterations of the Golgi apparatus may lead to phenotypes that human vision cannot easily discriminate. In this work, we present a high-content analysis framework including an unsupervised clustering step to automatically uncover Golgi phenotypic diversity. We use this deep phenotyping to quantitatively compare the effects of gene depletion.

Single-cell image analysis to explore cell-to-cell heterogeneity in isogenic populations

“…An unsupervised outlier detection approach identified HeLa cells with altered Golgi morphology, and after calculating phenotype penetrance for each gene and clustering of outlier cells, ten distinct phenotypic clusters were identified. This phenotypic information was used to build a Golgi phenotypic network that maps similarities between genetic perturbations (Hussain et al, 2017). Single-cell data have also been used to account for population context, such as the influence of neighboring cells, a concept that will also be crucial for informative analysis of more complex cell models (Liberali et al, 2014;Snijder et al, 2009Snijder et al, , 2012.…”

Evaluation of caridean ecological distribution in the Ubatuba region, southeastern Brazilian coast using unsupervised machine learning technique

“…This technique offers procedures that complement classic statistics, evaluating various topics such as ecologic distribution, population structure, and collective behavior (Valletta et al., 2017). Unsupervised procedures identify the data structure entrance and, using a cluster approach, reveal the groups/categories of data (Hussain et al., 2017). Previous studies, in different areas, utilized such technique for the creation of ethograms of seabirds (Sakamoto et al., 2009), evaluation of locomotion of wild lions and dogs (Dewhirst et al., 2017), and social interactions of rats (Unger et al., 2017).…”

A novel automated image analysis pipeline for quantifying morphological changes to the endoplasmic reticulum in cultured human cells

“…For example, although the Golgi complex is generally also a single organelle in mammalian cells, its appearance can be highly heterogeneous. Nevertheless, increasingly sophisticated image analysis routines are now able to report a variety of phenotypes seen in this organelle in response to various perturbations [4,5]. Similarly, in recent years excellent progress has been made in automated detection and analysis of other organelles displaying punctate and tubular morphologies, such as endosomes [6].…”