title: BLIND ordering of large-scale transcriptomic developmental timecourses.
abstract: RNA-Seq enables the efficient transcriptome sequencing of many samples from small amounts of material, but the analysis of these data remains challenging. In particular, in developmental studies, RNA-Seq is challenged by the morphological staging of samples, such as embryos, since these often lack clear markers at any particular stage. In such cases, the automatic identification of the stage of a sample would enable previously infeasible experimental designs. Here we present the 'basic linear index determination of transcriptomes' (BLIND) method for ordering samples comprising different developmental stages. The method is an implementation of a traveling salesman algorithm to order the transcriptomes according to their inter-relationships as defined by principal components analysis. To establish the direction of the ordered samples, we show that an appropriate indicator is the entropy of transcriptomic gene expression levels, which increases over developmental time. Using BLIND, we correctly recover the annotated order of previously published embryonic transcriptomic timecourses for frog, mosquito, fly and zebrafish. We further demonstrate the efficacy of BLIND by collecting 59 embryos of the sponge Amphimedon queenslandica and ordering their transcriptomes according to developmental stage. BLIND is thus useful in establishing the temporal order of samples within large datasets and is of particular relevance to the study of organisms with asynchronous development and when morphological staging is difficult.
authors: Department of Biology, Technion - Israel Institute of Technology, Haifa 32000, Israel.
authors: Leon
authors: L
authors: Anavy
authors: Michal
authors: M
authors: Levin
authors: Sally
authors: S
authors: Khair
authors: Nagayasu
authors: N
authors: Nakanishi
authors: Selene L
authors: SL
authors: Fernandez-Valverde
authors: Bernard M
authors: BM
authors: Degnan
authors: Itai
authors: I
authors: Yanai
mesh_terms: D000818:Animals; D020869:Gene Expression Profiling / Q000379:methods*; D018507:Gene Expression Regulation, Developmental; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D025341:Principal Component Analysis; D059467:Transcriptome / Q000235:genetics*
keywords: Amphimedon transcriptomic timecourse; Developmental timecourse; Large-scale datasets; Principal components analysis; Single-embryo RNA-Seq; Traveling salesman problem