Evidence map›Paper›PMID 29764375›Full record

ArticleBMC genomics2018

The aquatic animals' transcriptome resource for comparative functional analysis.

Chih-Hung Chou, Hsi-Yuan Huang, Wei-Chih Huang, Sheng-Da Hsu, Chung-Der Hsiao, Chia-Yu Liu, Yu-Hung Chen, Yu-Chen Liu, Wei-Yun Huang, Meng-Lin Lee and 2 more

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In one paragraph

Article in BMC genomics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

2 citing papers in PubMed.

  1. Article
  2. Exploiting the Freshwater ShrimpAntioxidants (Basel, Switzerland) · 2021
    Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

12 authors.

Chih-Hung ChouInstitute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 300, Taiwan.
Hsi-Yuan HuangInstitute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 300, Taiwan.
Wei-Chih HuangInstitute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 300, Taiwan.
Sheng-Da HsuInstitute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 300, Taiwan.
Chung-Der HsiaoDepartment of Bioscience Technology, Chung Yuan Christian University, Chungli, 320, Taiwan.
Chia-Yu LiuInstitute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 300, Taiwan.
Yu-Hung ChenInstitute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 300, Taiwan.
Yu-Chen LiuInstitute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 300, Taiwan.
Wei-Yun HuangDepartment of Biological Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan.
Meng-Lin LeeDepartment of Biological Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan.
Yi-Chang ChenInstitute of Molecular Medicine and Bioengineering, National Chiao Tung University, Hsinchu, 300, Taiwan.
Hsien-Da HuangInstitute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 300, Taiwan. bryan@mail.nctu.edu.tw.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

backgroundAquatic animals have great economic and ecological importance. Among them, non-model organisms have been studied regarding eco-toxicity, stress biology, and environmental adaptation. Due to recent advances in next-generation sequencing techniques, large amounts of RNA-seq data for aquatic animals are publicly available. However, currently there is no comprehensive resource exist for the analysis, unification, and integration of these datasets. This study utilizes computational approaches to build a new resource of transcriptomic maps for aquatic animals. This aquatic animal transcriptome map database dbATM provides de novo assembly of transcriptome, gene annotation and comparative analysis of more than twenty aquatic organisms without draft genome.

resultsTo improve the assembly quality, three computational tools (Trinity, Oases and SOAPdenovo-Trans) were employed to enhance individual transcriptome assembly, and CAP3 and CD-HIT-EST software were then used to merge these three assembled transcriptomes. In addition, functional annotation analysis provides valuable clues to gene characteristics, including full-length transcript coding regions, conserved domains, gene ontology and KEGG pathways. Furthermore, all aquatic animal genes are essential for comparative genomics tasks such as constructing homologous gene groups and blast databases and phylogenetic analysis.

conclusionIn conclusion, we establish a resource for non model organism aquatic animals, which is great economic and ecological importance and provide transcriptomic information including functional annotation and comparative transcriptome analysis. The database is now publically accessible through the URL http://dbATM.mbc.nctu.edu.tw/ .

Indexed as

AnimalsAquatic OrganismsDatabases, GeneticGene Expression ProfilingGene Regulatory NetworksGenomicsHigh-Throughput Nucleotide SequencingMolecular Sequence AnnotationPhylogenySequence Analysis, RNASoftware

Identifiers

PMID29764375
PMCPMC5954267

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.