title: Pan-transcriptomic analysis identifies coordinated and orthologous functional modules in the diatoms Thalassiosira pseudonana and Phaeodactylum tricornutum.
abstract: Diatoms are important primary producers in the ocean that thrive in diverse and dynamic environments. Their survival and success over changing conditions depend on the complex coordination of gene regulatory processes. Here we present an integrated analysis of all publicly available microarray data for the diatoms Thalassiosira pseudonana and Phaeodactylum tricornutum. This resource includes shared expression patterns, gene functions, and cis-regulatory DNA sequence motifs in each species that are statistically coordinated over many experiments. These data illustrate the coordination of transcriptional responses in diatoms over changing environmental conditions. Responses to silicic acid depletion segregate into multiple distinctly regulated groups of genes, regulation by heat shock transcription factors (HSFs) is implicated in the response to nitrate stress, and distinctly coordinated carbon concentrating, CO2 and pH-related responses are apparent. Fundamental features of diatom physiology are similarly coordinated between two distantly related diatom species, including the regulation of photosynthesis, cellular growth functions and lipid metabolism. These integrated data and analyses can be explored publicly (http://networks.systemsbiology.net/diatom-portal/).
authors.affiliation: Institute for Systems Biology, Seattle, WA, USA. Electronic address: ashwortj@uw.edu.
authors.forename: Justin
authors.initials: J
authors.lastname: Ashworth
authors.affiliation: Institute for Systems Biology, Seattle, WA, USA.
authors.forename: Serdar
authors.initials: S
authors.lastname: Turkarslan
authors.affiliation: Institute for Systems Biology, Seattle, WA, USA.
authors.forename: Micheleen
authors.initials: M
authors.lastname: Harris
authors.affiliation: Institute for Systems Biology, Seattle, WA, USA; Polar Science Center, University of Washington, Seattle, WA, USA.
authors.forename: Mónica V
authors.initials: MV
authors.lastname: Orellana
authors.affiliation: Institute for Systems Biology, Seattle, WA, USA; Department of Microbiology, University of Washington, Seattle, WA, USA. Electronic address: nitin.baliga@systemsbiology.org.
authors.forename: Nitin S
authors.initials: NS
authors.lastname: Baliga
mesh_terms: D016000:Cluster Analysis; D017377:Diatoms / Q000235:genetics*; D005786:Gene Expression Regulation / Q000502:physiology*; D010802:Phylogeny; D059467:Transcriptome
keywords: Clustering; Diatom; Gene regulation; Microarrays; Transcriptomics