PT - JOURNAL ARTICLE AU - Lynn Yi AU - Harold Pimentel AU - Lior Pachter TI - Zika infection of neural progenitor cells perturbs transcription in neurodevelopmental pathways AID - 10.1101/072439 DP - 2016 Jan 01 TA - bioRxiv PG - 072439 4099 - http://biorxiv.org/content/early/2016/09/02/072439.short 4100 - http://biorxiv.org/content/early/2016/09/02/072439.full AB - Background A recent study of the gene expression patterns of Zika virus (ZIKV) infected human neural progenitor cells (hNPCs) revealed transcriptional dysregulation and identified cell-cycle-related pathways that are affected by infection. However deeper exploration of the information present in the RNA-Seq data can be used to further elucidate the manner in which Zika infection of hNPCs affects the transcriptome, refining pathway predictions and revealing isoform-specific dynamics.Methodology/Principal Findings We analyzed data published by Tang et al. using state-of-the-art tools for transcriptome analysis. By accounting for the experimental design and estimation of technical and inferential variance we were able to pinpoint Zika infection affected pathways that highlight Zika’s neural tropism. The examination of differential genes reveals cases of isoform divergence.Conclusions/Significance Transcriptome analysis of Zika infected hNPCs has the potential to identify the molecular signatures of Zika infected neural cells. These signatures may be useful for diagnostics and for the resolution of infection pathways that can be used to harvest specific targets for further study.