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Plant Cell Physiol. 2016 Jan;57(1):e3. doi: 10.1093/pcp/pcv190. Epub 2015 Dec 7.

ALCOdb: Gene Coexpression Database for Microalgae.

Author information

1
Graduate School of Information Sciences, Tohoku University, 6-3-09, Aramaki-Aza-Aoba, Aoba-ku, Sendai, 980-8579 Japan Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Kawaguchi, Saitama, Japan.
2
Graduate School of Information Sciences, Tohoku University, 6-3-09, Aramaki-Aza-Aoba, Aoba-ku, Sendai, 980-8579 Japan.
3
Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Kawaguchi, Saitama, Japan Department of Biological Sciences, Tokyo Institute of Technology, Yokohama, Kanagawa, 226-8501 Japan Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8551 Japan.
4
Graduate School of Information Sciences, Tohoku University, 6-3-09, Aramaki-Aza-Aoba, Aoba-ku, Sendai, 980-8579 Japan Institute of Development, Aging, and Cancer, Tohoku University, Sendai, 980-8575 Japan Tohoku Medical Megabank Organization, Tohoku University, Sendai, 980-8573 Japan.
5
Graduate School of Information Sciences, Tohoku University, 6-3-09, Aramaki-Aza-Aoba, Aoba-ku, Sendai, 980-8579 Japan Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Kawaguchi, Saitama, Japan obayashi@ecei.tohoku.ac.jp.

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.

KEYWORDS:

Chlamydomonas reinhardtii; Comparative transcriptomics; Cyanidioschyzon merolae; Database; Gene coexpression; Microalgae

PMID:
26644461
PMCID:
PMC4722175
DOI:
10.1093/pcp/pcv190
[Indexed for MEDLINE]
Free PMC Article

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