SARS-CoV-2 transcriptomic consensome - full

This network ranks human genes by the significance of their differential expression (p < 0.05) across multiple independent public archived experiments involving infection of human cells by SARS-CoV-2. For an introduction to consensome analysis please refer to Ochsner et al. (2019) Nat Sci Data 6, 252 METHODS The frequency of differential expression (p < 0.05) of human gene targets (discovery rate) was calculated across publicly archived transcriptomic experiments involving infection of a human cell line with different viruses. The consensome p-value (and FDR-corrected q-value) correspond to the probability that this frequency is a random event. Genes are ranked in ascending order of consensome q-value and organized into percentiles, such that the 99th percentile contains the genes with the lowest consensome q-value. The higher the percentile, the greater the confidence of a transcriptional regulatory relationship between CoV infection and a target gene. INTERPRETATION Viral transcriptional targets in this network are organized according to SPP’s signaling pathway node-centric classification, which classifies mammalian genes as encoding receptors, enzymes, transcription factors, ion channels or co-nodes. Target genes (circles) are colored according to the category of factor they encode: orange = receptors; blue = enzymes; green = transcription factors; mustard = ion channels; grey = co-nodes. Target genes are sorted into classes (white rectangles) of each category. Circle sizes are proportional to the PERCENTILE: the larger the circle, the lower the q-value and the greater the confidence that a gene target is regulated in response to infection by that virus. Clicking a gene target will pull up a pane showing details on the data point, including details such as the family to which it belongs, and a link to the underlying data points on the SPP website. This network contains the full consensome data; however, for an effective visualization, the custom sample displays only genes with a PERCENTILE value equal or greater than 95 (top 5%). The network for the 95th PERCENTILE subset is available HERE. DATASETS The datasets underlying this consensome can be accessed at: https://www.signalingpathways.org/datasets/index.jsf