Inferring cellular and molecular processes in single-cell data with non-negative matrix factorization using Python, R and GenePattern Notebook implementations of CoGAPS.

Non-negative matrix factorization (NMF) is an unsupervised learning method well suited to high-throughput biology. However, inferring biological processes from an NMF result still requires additional post hoc statistics and annotation for interpretation of learned features. Here, we introduce a suite of computational tools that implement NMF and provide methods for accurate and clear biological interpretation and analysis. A generalized discussion of NMF covering its benefits, limitations and open questions is followed by four procedures for the Bayesian NMF algorithm Coordinated Gene Activity across Pattern Subsets (CoGAPS). Each procedure will demonstrate NMF analysis to quantify cell state transitions in a public domain single-cell RNA-sequencing dataset. The first demonstrates PyCoGAPS, our new Python implementation that enhances runtime for large datasets, and the second allows its deployment in Docker. The third procedure steps through the same single-cell NMF analysis using our R CoGAPS interface. The fourth introduces a beginner-friendly CoGAPS platform using GenePattern Notebook, aimed at users with a working conceptual knowledge of data analysis but without a basic proficiency in the R or Python programming language. We also constructed a user-facing website to serve as a central repository for information and instructional materials about CoGAPS and its application programming interfaces. The expected timing to setup the packages and conduct a test run is around 15 min, and an additional 30 min to conduct analyses on a precomputed result. The expected runtime on the user's desired dataset can vary from hours to days depending on factors such as dataset size or input parameters.

Peripheral blood mononuclear cell production of TNF-alpha in response to North American ginseng stimulation.

North American ginseng (Panax quinquefolium) root extract (NAGE) with known ginsenosides composition was examined for its affinity to stimulate human tumour necrosis factor alpha (TNF-alpha) production in human peripheral blood mononuclear cells. Case studies were conducted in three donors, one that was diagnosed with an atopic allergy and two that were normal, healthy subjects. Cultured mononuclear cells were incubated with varying concentrations of NAGE for up to 72 h and culture media were tested for TNF-alpha concentration. Direct stimulation of mononuclear cell TNF-alpha production in vitro by NAGE occurred as early as 6 h with 200 microg NAGE/mL. The stimulation of TNF-alpha production was confirmed by TNF-alpha mRNA gene expression. These interesting results show the immunostimulating activity of NAGE components in reference to TNF-alpha production. This observation requires further investigation with more subjects to determine the affinity of ginseng in stimulating the human immune system. Moreover, the method of evaluating this response is very useful for standardizing ginseng extracts to a known bioactivity.