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Cited by 43Algal biology and biofuel productionBioinformatics and Genomic NetworksGenomics and Phylogenetic Studies

ALCOdb: Gene Coexpression Database for Microalgae

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Aoki, Yuichi, Okamura, Yasunobu, Ohta, Hiroyuki, Kinoshita, Kengo, Obayashi, Takeshi·2016·Plant and Cell Physiology
DOI 10.1093/pcp/pcv190PMC PMC4722175
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Abstract

In the era of energy and food shortage, microalgae have gained much attention as promising sources of biofuels and food ingredients. However, only a small fraction of microalgal genes have been functionally characterized. Here, we have developed the Algae Gene Coexpression database (ALCOdb; http://alcodb.jp), which provides gene coexpression information to survey gene modules for a function of interest. ALCOdb currently supports two model algae: the green alga Chlamydomonas reinhardtii and the red alga Cyanidioschyzon merolae. Users can retrieve coexpression information for genes of interest through three unique data pages: (i) Coexpressed Gene List; (ii) Gene Information; and (iii) Coexpressed Gene Network. In addition to the basal coexpression information, ALCOdb also provides several advanced functionalities such as an expression profile viewer and a differentially expressed gene search tool. Using these user interfaces, we demonstrated that our gene coexpression data have the potential to detect functionally related genes and are useful in extrapolating the biological roles of uncharacterized genes. ALCOdb will facilitate molecular and biochemical studies of microalgal biological phenomena, such as lipid metabolism and organelle development, and promote the evolutionary understanding of plant cellular systems.

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  • Three web-based resources for algal genomics (pico-PLAZA, AlgaePath, ALCOdb) provide genomic information, intuitive tools for functional genomics, gene co-expression data, and details of gene expression prediction based on metabolic pathways in some microalgae.

    “Besides, there are three web-based resources available for algal genomics, including pico-PLAZA (http://bioinformatics.psb.ugent.be/pico-plaza/), AlgaePath (http://algaepath.itps.ncku.edu.tw), and ALCOdb (http://alcodb.jp). These genomics resources provide genomic information, intuitive tools for functional genomics, gene co-expression data, and details of gene expression prediction based on metab”

    From Microalgae biofuels: illuminating the path to a sustainable future amidst challenges and opportunities (2024) · cites this paper as [227]

    The Introduction and Results and Discussion (no page numbers available) identify ALCOdb as a web-based microalgal resource with gene co-expression data and tools for investigating gene function; the Introduction also describes AlgaePath. Our copy does not establish the claim about pico-PLAZA or describe gene-expression prediction based on metabolic pathways. (LLM, conf=0.86)

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Authors
Aoki, Y., Okamura, Y., Ohta, H., Kinoshita, K., & Obayashi, T.
Affiliations
  • Tohoku University (JP)
  • Tokyo Institute of Technology (JP)
Corresponding author
Obayashi, Takeshi
ORCID
Venue
Plant and Cell Physiology
Publisher
Oxford University Press (OUP)
Published
2015-12-07
Volume
57
Issue
1
Pages
e3-e3
ISSN
  • 0032-0781 (ISSN-L)
  • 1471-9053
DOI
10.1093/pcp/pcv190
PMC
PMC4722175
OpenAlex
W2190741296
Cited by
43
References
3
Citations by year
2026: 1 · 2025: 2 · 2024: 6 · 2023: 2 · 2022: 3 · 2021: 9 · 2020: 7 · 2019: 4 · 2018: 2 · 2017: 4 · 2016: 3
FWCI
0.89
Type
journal article
Language
en
Open access
Licence
cc-by
Locations
  • Plant and Cell Physiology (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • HighWire Press Open Archive (submittedVersion)
  • Tokyo Tech Research Repository (Tokyo Institute of Technology) (submittedVersion)
Funders
  • Japan Science and Technology Corporation (CREST)
  • Japan Society for the Promotion of Science (15K18464, 15K20863, 24114001, 24114005)
  • Core Research for Evolutional Science and Technology
Topics
  • Physical Sciences › Energy › Renewable Energy, Sustainability and the Environment › Algal biology and biofuel production
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Keywords
gene co-expression, microalgae, Chlamydomonas reinhardtii, Cyanidioschyzon merolae, gene co-expression network, gene function prediction, differentially expressed genes, gene expression patterns, lipid metabolism, organelle development, biofuels
MeSH terms
Rhodophyta, User-Computer Interface, Chlamydomonas reinhardtii, Databases, Genetic, Lipid Metabolism, Gene Regulatory Networks, Microalgae, Transcriptome

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