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Network analysis reveals stage-specific changes in zebrafish embryo development using time course whole transcriptome profiling and prior biological knowledge

Overview of attention for article published in BioData Mining, August 2015
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  • Good Attention Score compared to outputs of the same age (66th percentile)

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5 tweeters


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18 Mendeley
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Network analysis reveals stage-specific changes in zebrafish embryo development using time course whole transcriptome profiling and prior biological knowledge
Published in
BioData Mining, August 2015
DOI 10.1186/s13040-015-0057-1
Pubmed ID

Yuji Zhang


Molecular networks act as the backbone of molecular activities within cells, offering a unique opportunity to better understand the mechanism of diseases. While network data usually constitute only static network maps, integrating them with time course gene expression information can provide clues to the dynamic features of these networks and unravel the mechanistic driver genes characterizing cellular responses. Time course gene expression data allow us to broadly "watch" the dynamics of the system. However, one challenge in the analysis of such data is to establish and characterize the interplay among genes that are altered at different time points in the context of a biological process or functional category. Integrative analysis of these data sources will lead us a more complete understanding of how biological entities (e.g., genes and proteins) coordinately perform their biological functions in biological systems. In this paper, we introduced a novel network-based approach to extract functional knowledge from time-dependent biological processes at a system level using time course mRNA sequencing data in zebrafish embryo development. The proposed method was applied to investigate 1α, 25(OH)2D3-altered mechanisms in zebrafish embryo development. We applied the proposed method to a public zebrafish time course mRNA-Seq dataset, containing two different treatments along four time points. We constructed networks between gene ontology biological process categories, which were enriched in differential expressed genes between consecutive time points and different conditions. The temporal propagation of 1α, 25-Dihydroxyvitamin D3-altered transcriptional changes started from a few genes that were altered initially at earlier stage, to large groups of biological coherent genes at later stages. The most notable biological processes included neuronal and retinal development and generalized stress response. In addition, we also investigated the relationship among biological processes enriched in co-expressed genes under different conditions. The enriched biological processes include translation elongation, nucleosome assembly, and retina development. These network dynamics provide new insights into the impact of 1α, 25-Dihydroxyvitamin D3 treatment in bone and cartilage development. We developed a network-based approach to analyzing the DEGs at different time points by integrating molecular interactions and gene ontology information. These results demonstrate that the proposed approach can provide insight on the molecular mechanisms taking place in vertebrate embryo development upon treatment with 1α, 25(OH)2D3. Our approach enables the monitoring of biological processes that can serve as a basis for generating new testable hypotheses. Such network-based integration approach can be easily extended to any temporal- or condition-dependent genomic data analyses.

Twitter Demographics

The data shown below were collected from the profiles of 5 tweeters who shared this research output. Click here to find out more about how the information was compiled.

Mendeley readers

The data shown below were compiled from readership statistics for 18 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 18 100%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 6 33%
Researcher 3 17%
Professor > Associate Professor 2 11%
Student > Bachelor 2 11%
Student > Master 2 11%
Other 3 17%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 5 28%
Agricultural and Biological Sciences 4 22%
Engineering 2 11%
Computer Science 2 11%
Medicine and Dentistry 1 6%
Other 2 11%
Unknown 2 11%

Attention Score in Context

This research output has an Altmetric Attention Score of 3. 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 01 September 2015.
All research outputs
of 5,579,069 outputs
Outputs from BioData Mining
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Outputs of similar age
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Outputs of similar age from BioData Mining
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Altmetric has tracked 5,579,069 research outputs across all sources so far. This one has received more attention than most of these and is in the 62nd percentile.
So far Altmetric has tracked 152 research outputs from this source. They typically receive more attention than average, with a mean Attention Score of 7.7. This one is in the 42nd percentile – i.e., 42% of its peers scored the same or lower than it.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 195,046 tracked outputs that were published within six weeks on either side of this one in any source. This one has gotten more attention than average, scoring higher than 66% of its contemporaries.
We're also able to compare this research output to 9 others from the same source and published within six weeks on either side of this one. This one has scored higher than 2 of them.