BLIND ordering of large-scale transcriptomic developmental timecourses

Anavy, Leon, Levin, Michal, Khair, Sally, Nakanishi, Nagayasu, Fernandez-Valverde, Selene L., Degnan, Bernard M. and Yanai, Itai (2014) BLIND ordering of large-scale transcriptomic developmental timecourses. Development (Cambridge), 141 5: 1161-1166. doi:10.1242/dev.105288

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Author Anavy, Leon
Levin, Michal
Khair, Sally
Nakanishi, Nagayasu
Fernandez-Valverde, Selene L.
Degnan, Bernard M.
Yanai, Itai
Title BLIND ordering of large-scale transcriptomic developmental timecourses
Journal name Development (Cambridge)   Check publisher's open access policy
ISSN 0950-1991
1477-9129
Publication date 2014-03-01
Sub-type Article (original research)
DOI 10.1242/dev.105288
Open Access Status File (Publisher version)
Volume 141
Issue 5
Start page 1161
End page 1166
Total pages 6
Place of publication Cambridge, United Kingdom
Publisher The Company of Biologists Ltd.
Language eng
Subject 1309 Developmental Biology
1312 Molecular Biology
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.
Keyword Amphimedon transcriptomic timecourse
Developmental timecourse
Large scale datasets
Principal components analysis
Single embryo RNA seq
Traveling salesman problem
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: Official 2015 Collection
School of Biological Sciences Publications
Centre for Marine Studies Publications
 
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