Pop's Pipes: Poplar Gene Expression Data Analysis Pipelines

We developed multiple web-based gene expression data analysis pipelines called Pop’s pipes for rapidly preprocessing and analyzing substantial amount of microarray or RNA-seq gene expression data in model woody plant species, poplar. We constructed multiple web portals through which we have made all pipelines available to research community. The package includes the pipelines for identification of differentially expressed genes, pathways analysis, gene ontology enrichment analysis, protein domain analysis, and construction of gene ontology tree. The automated pipelines can be used to analyze large amount of gene expression data from multiple sets of paired data from comparable tissues, time points, or treatment-verse-control data in a single run. The Pop’s pipes can potentially save users tremendous time, and produce error-prone outputs when large numbers of comparative data sets are needs to be analyzed.