Carrasco Pro, S. | bioRxiv Science

bioRxiv2018

Interactive single cell RNA-Seq analysis with the Single Cell Toolkit (SCTK)

Single cell RNA-sequencing (scRNA-Seq) allows researchers to profile transcriptional activity in individual cells. However, the complex nature of these data and variability in study design and data generation requires sophisticated computational tools and informed analytical decisions. Here, we present the Single Cell Toolkit (SCTK), an interactive scRNA-Seq analysis package that enables users to perform scRNA-Seq analysis interactively using a command-line workflow or a graphical user interface (GUI) written in R/Shiny.

bioinformatics↗

bioRxiv2018

Global landscape of mouse and human cytokine transcriptional regulation

Cytokines play a central role in immune development, pathogen responses, and diseases. Cytokines are highly regulated at the transcriptional level by combinations of transcription factors (TFs) that recruit cofactors and the transcriptional machinery. Here, we review three decades of studies to generate a comprehensive database reporting 843 and 647 interactions between TFs and cytokines genes, in human and mouse respectively (http://cytreg.bu.edu). We provide a historic perspective on cytokine regulation discussing research trends and biases. More importantly, by integrating this comprehensive database with other functional datasets, we determine general principles governing the transcriptional regulation of cytokine genes. In particular, we show a correlation between TF connectivity and immune phenotype and disease, we discuss the balance between tissue-specific and pathogen-activated TFs regulating each cytokine gene, and cooperativity and plasticity in cytokine regulation. Finally, we illustrate the use of our database as a blueprint to study TF-cytokine regulatory axes in autoimmune diseases.

immunology↗