Supporting data for "Defining the characteristics of interferon-alpha-stimulated human genes: insight from expression data and machine-learning"

A virus-infected cell triggers a signalling cascade resulting in the secretion of interferons (IFNs), which in turn induces the up-regulation of the IFN stimulated genes (ISGs) that play a role in anti-pathogen host defence. Here, we conducted analyses on large-scale data relating to evolutionary, gene expression, sequence composition, and network properties to elucidate factors associated with the stimulation of human genes in response to IFN-. <br>We find that ISGs are less evolutionary conserved than genes that are not significantly stimulated in IFN experiments (non-ISGs). ISGs show obvious depletion of GC-content in the coding region. This influences the representation of some compositions following the translation process. IFN repressed human genes (IRGs), down-regulated genes in IFN experiments, can have similar properties to the ISGs. Additionally, we design a machine-learning framework integrating the support vector machine and novel feature selection algorithm that achieves an area under the receiver operating characteristic curve (AUC) of 0.7455 for ISG prediction. Its application in other IFN-systems suggests the similarity between the ISGs triggered by type I and III IFNs. <br> ISGs have some unique properties that make them different from the non-ISGs. The representation of some properties have strong correlations with genes expression following IFN- stimulation, which can be used as predictive features in machine learning. Our model predicts several genes as putative ISGs that so far have shown no significant differential expression when stimulated with IFN- in the cell/tissue types in the available databases. A webserver implementing our method is accessible at http://isgpre.cvr.gla.ac.uk/. The docker image at https://hub.docker.com/r/hchai01/isgpre can be downloaded to reproduce the prediction.