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Fish connectivity mapping: linking chemical stressors by their mechanisms of action-driven transcriptomic profiles

Overview of attention for article published in BMC Genomics, January 2016
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Title
Fish connectivity mapping: linking chemical stressors by their mechanisms of action-driven transcriptomic profiles
Published in
BMC Genomics, January 2016
DOI 10.1186/s12864-016-2406-y
Pubmed ID
Authors

Rong-Lin Wang, Adam D. Biales, Natalia Garcia-Reyero, Edward J. Perkins, Daniel L. Villeneuve, Gerald T. Ankley, David C. Bencic

Abstract

A very large and rapidly growing collection of transcriptomic profiles in public repositories is potentially of great value to developing data-driven bioinformatics applications for toxicology/ecotoxicology. Modeled on human connectivity mapping (Cmap) in biomedical research, this study was undertaken to investigate the utility of an analogous Cmap approach in ecotoxicology. Over 3500 zebrafish (Danio rerio) and fathead minnow (Pimephales promelas) transcriptomic profiles, each associated with one of several dozen chemical treatment conditions, were compiled into three distinct collections of rank-ordered gene lists (ROGLs) by species and microarray platforms. Individual query signatures, each consisting of multiple gene probes differentially expressed in a chemical condition, were used to interrogate the reference ROGLs. Informative connections were established at high success rates within species when, as defined by their mechanisms of action (MOAs), both query signatures and ROGLs were associated with the same or similar chemicals. Thus, a simple query signature functioned effectively as an exposure biomarker without need for a time-consuming process of development and validation. More importantly, a large reference database of ROGLs also enabled a query signature to cross-interrogate other chemical conditions with overlapping MOAs, leading to novel groupings and subgroupings of seemingly unrelated chemicals at a finer resolution. This approach confirmed the identities of several estrogenic chemicals, as well as a polycyclic aromatic hydrocarbon and a neuro-toxin, in the largely uncharacterized water samples near several waste water treatment plants, and thus demonstrates its future potential utility in real world applications. The power of Cmap should grow as chemical coverages of ROGLs increase, making it a framework easily scalable in the future. The feasibility of toxicity extrapolation across fish species using Cmap needs more study, however, as more gene expression profiles linked to chemical conditions common to multiple fish species are needed.

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Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 37 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 37 100%

Demographic breakdown

Readers by professional status Count As %
Student > Master 9 24%
Student > Ph. D. Student 8 22%
Researcher 5 14%
Student > Doctoral Student 3 8%
Student > Postgraduate 2 5%
Other 2 5%
Unknown 8 22%
Readers by discipline Count As %
Agricultural and Biological Sciences 10 27%
Environmental Science 3 8%
Biochemistry, Genetics and Molecular Biology 3 8%
Computer Science 2 5%
Medicine and Dentistry 2 5%
Other 3 8%
Unknown 14 38%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 1. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 30 January 2016.
All research outputs
#17,783,561
of 22,842,950 outputs
Outputs from BMC Genomics
#7,569
of 10,655 outputs
Outputs of similar age
#270,063
of 396,721 outputs
Outputs of similar age from BMC Genomics
#226
of 275 outputs
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