Knowledge synthesis from 100 million biomedical documents augments the deep expression profiling of coronavirus receptors

AJ Venkatakrishnan; Arjun Puranik; Akash Anand; David Zemmour; Xiang Yao; Xiaoying Wu; Ramakrishna Chilaka; Dariusz K Murakowski; Kristopher Standish; Bharathwaj Raghunathan; Tyler Wagner; Enrique Garcia-Rivera; Hugo Solomon; Abhinav Garg; Rakesh Barve; Anuli Anyanwu-Ofili; Najat Khan; Venky Soundararajan

The platform allows users to query any gene in any selected study. The corresponding data is displayed in commonly employed formats including a series of violin plots and as a set of dimensionality reduction plots. Expression is summarized by listing the percent of cells expressing Gene G in each annotated cluster and the mean expression of Gene G in each cluster. To measure the specificity of Gene G expression to each Cluster C, we compute a cohen's D value which assesses the effect size between the mean expression of Gene G in cluster C and the mean expression of Gene G in all other clusters. Specifically, the cohen's D formula is given as follows: (MeanC -MeanA)/(sqrt(StDevC 2 + StDevA 2 )), where C represents the cluster of interest and A represents the complement of C (i.e. all other cell clusters). Note that this is functionally similar to the computation of paired fold change values and p-values between clusters which is frequently used to identify cluster-defining genes.