We developed multiple gene expression pipelines and assembled them into a web-based tool called Pop’s Pipes to facilitate preprocessing and analysis of substantial poplar gene expression data. The input data can be spatiotemporal microarray and RNA-seq data from comparable tissues, time points, or treatment-vs-control conditions. Pop’s Pipes can be used to identify differentially expressed genes between one or multiple paired tissues, time points, or treatment-vs-control conditions in a single in silico analysis. The differentially expressed genes (DEGs) obtained for each comparison will be automatically analyzed by Pop’s Pipes for identifying significantly enriched gene ontologies and interpro protein domains. Also, significantly changed metabolic pathways across all input data sets will be identified. We also integrated a pipeline into Pop's Pipes for constructing any of three type gene ontology trees when a short list of gene ontologies from biological processes, molecular functions, or cellular components is used as an input. The resulting information from Pop’s Pipes enables scrutiny to create spatiotemporal models and hypotheses to understand how poplar develops and functions. Pop’s Pipes can analyze a microarray or RNA-seq data set with 10 time points in 4–10 h, with each time point containing three replicates of treatments and three controls. Such a data set usually takes a bioinformatician a few months to a year to analyze. Pop’s Pipes can thus save users tremendous amounts of research time when large numbers of comparative data need to be analyzed.
Poplar Microarray RNA-seq data Differentially expressed genes Pathway enrichment analysis Gene ontology enrichment analysis Protein domain enrichment analysis Pipeline Gene ontology tree
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We thank James Bialas for setting up and configuring the server. This project was partly supported with a start-up fund to Dr. Wei from the School of Forest Resources and Environment Science, Michigan Technological University; a grant from the Plant Feedstock Genomics for Bioenergy: A Joint Research Program of USDA and DOE (2009-65504-05767, ER65454-1040591-0018445) to V. B.; and also the National Science Foundation Plant Genome Research Program Grant (DBI-0922391) to V.L.C.
Data archiving statement
RNA-seq data from Ptr-miR397a transgenic lines that were used to test Pop’s pipelines have been deposited into the Gene Expression Omnibus (GEO) database at NCBI (http://www.ncbi.nlm.nih.gov/geo/) with the accession number GSE54153. The data will be available after this manuscript is accepted. The microarray data of Populus deltoides were not our own data, and these data have been published in GEO database with an ID of GSE24349.
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