↓ Skip to main content

GigaTON: an extensive publicly searchable database providing a new reference transcriptome in the pacific oyster Crassostrea gigas

Overview of attention for article published in BMC Bioinformatics, December 2015
Altmetric Badge

About this Attention Score

  • In the top 25% of all research outputs scored by Altmetric
  • High Attention Score compared to outputs of the same age (84th percentile)
  • High Attention Score compared to outputs of the same age and source (86th percentile)

Mentioned by

blogs
1 blog
twitter
5 tweeters

Citations

dimensions_citation
28 Dimensions

Readers on

mendeley
61 Mendeley
citeulike
1 CiteULike
You are seeing a free-to-access but limited selection of the activity Altmetric has collected about this research output. Click here to find out more.
Title
GigaTON: an extensive publicly searchable database providing a new reference transcriptome in the pacific oyster Crassostrea gigas
Published in
BMC Bioinformatics, December 2015
DOI 10.1186/s12859-015-0833-4
Pubmed ID
Authors

Guillaume Riviere, Christophe Klopp, Nabihoudine Ibouniyamine, Arnaud Huvet, Pierre Boudry, Pascal Favrel

Abstract

The Pacific oyster, Crassostrea gigas, is one of the most important aquaculture shellfish resources worldwide. Important efforts have been undertaken towards a better knowledge of its genome and transcriptome, which makes now C. gigas becoming a model organism among lophotrochozoans, the under-described sister clade of ecdysozoans within protostomes. These massive sequencing efforts offer the opportunity to assemble gene expression data and make such resource accessible and exploitable for the scientific community. Therefore, we undertook this assembly into an up-to-date publicly available transcriptome database: the GigaTON (Gigas TranscriptOme pipeliNe) database. We assembled 2204 million sequences obtained from 114 publicly available RNA-seq libraries that were realized using all embryo-larval development stages, adult organs, different environmental stressors including heavy metals, temperature, salinity and exposure to air, which were mostly performed as part of the Crassostrea gigas genome project. This data was analyzed in silico and resulted into 56621 newly assembled contigs that were deposited into a publicly available database, the GigaTON database. This database also provides powerful and user-friendly request tools to browse and retrieve information about annotation, expression level, UTRs, splice and polymorphism, and gene ontology associated to all the contigs into each, and between all libraries. The GigaTON database provides a convenient, potent and versatile interface to browse, retrieve, confront and compare massive transcriptomic information in an extensive range of conditions, tissues and developmental stages in Crassostrea gigas. To our knowledge, the GigaTON database constitutes the most extensive transcriptomic database to date in marine invertebrates, thereby a new reference transcriptome in the oyster, a highly valuable resource to physiologists and evolutionary biologists.

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 61 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Japan 1 2%
France 1 2%
South Africa 1 2%
Unknown 58 95%

Demographic breakdown

Readers by professional status Count As %
Researcher 20 33%
Student > Master 9 15%
Student > Ph. D. Student 8 13%
Student > Bachelor 7 11%
Professor > Associate Professor 4 7%
Other 8 13%
Unknown 5 8%
Readers by discipline Count As %
Agricultural and Biological Sciences 31 51%
Biochemistry, Genetics and Molecular Biology 14 23%
Environmental Science 6 10%
Veterinary Science and Veterinary Medicine 1 2%
Computer Science 1 2%
Other 2 3%
Unknown 6 10%

Attention Score in Context

This research output has an Altmetric Attention Score of 9. 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 08 December 2015.
All research outputs
#2,511,077
of 16,638,522 outputs
Outputs from BMC Bioinformatics
#954
of 5,984 outputs
Outputs of similar age
#59,037
of 370,937 outputs
Outputs of similar age from BMC Bioinformatics
#65
of 472 outputs
Altmetric has tracked 16,638,522 research outputs across all sources so far. Compared to these this one has done well and is in the 84th percentile: it's in the top 25% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 5,984 research outputs from this source. They typically receive a little more attention than average, with a mean Attention Score of 5.1. This one has done well, scoring higher than 84% of its peers.
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 370,937 tracked outputs that were published within six weeks on either side of this one in any source. This one has done well, scoring higher than 84% of its contemporaries.
We're also able to compare this research output to 472 others from the same source and published within six weeks on either side of this one. This one has done well, scoring higher than 86% of its contemporaries.