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Plant Cell Physiol. 2015 Jan;56(1):e9. doi: 10.1093/pcp/pcu188. Epub 2014 Dec 11.

Plant Omics Data Center: an integrated web repository for interspecies gene expression networks with NLP-based curation.

Author information

1
School of Agriculture, Meiji University, Kawasaki, 214-8571 Japan CREST, JST, Saitama, 332-0012 Japan Tsukuba Division, Mitsubishi Space Software Co., Ltd., Tsukuba, 305-0032 Japan Plant Genetics Laboratory, National Institute of Genetics, Mishima, 411-8540 Japan These authors contributed equally to this work.
2
School of Agriculture, Meiji University, Kawasaki, 214-8571 Japan CREST, JST, Saitama, 332-0012 Japan These authors contributed equally to this work.
3
School of Agriculture, Meiji University, Kawasaki, 214-8571 Japan CREST, JST, Saitama, 332-0012 Japan.
4
School of Agriculture, Meiji University, Kawasaki, 214-8571 Japan.
5
Bioscience and Biotechnology Center, Nagoya University, Nagoya, 464-8601 Japan.
6
Graduate School of Bioresources, Mie University, Tsu, 514-8507 Japan.
7
Division of Natural Science, Osaka Kyoiku University, Kashiwara, 582-8582 Japan.
8
Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai, 599-8531 Japan.
9
Graduate School of Environmental and Life Science, Okayama University, Okayama, 700-8530 Japan.
10
Graduate School of Life Sciences, Tohoku University, Sendai, 980-8577 Japan.
11
School of Agriculture, Meiji University, Kawasaki, 214-8571 Japan CREST, JST, Saitama, 332-0012 Japan kyano@isc.meiji.ac.jp.

Abstract

Comprehensive integration of large-scale omics resources such as genomes, transcriptomes and metabolomes will provide deeper insights into broader aspects of molecular biology. For better understanding of plant biology, we aim to construct a next-generation sequencing (NGS)-derived gene expression network (GEN) repository for a broad range of plant species. So far we have incorporated information about 745 high-quality mRNA sequencing (mRNA-Seq) samples from eight plant species (Arabidopsis thaliana, Oryza sativa, Solanum lycopersicum, Sorghum bicolor, Vitis vinifera, Solanum tuberosum, Medicago truncatula and Glycine max) from the public short read archive, digitally profiled the entire set of gene expression profiles, and drawn GENs by using correspondence analysis (CA) to take advantage of gene expression similarities. In order to understand the evolutionary significance of the GENs from multiple species, they were linked according to the orthology of each node (gene) among species. In addition to other gene expression information, functional annotation of the genes will facilitate biological comprehension. Currently we are improving the given gene annotations with natural language processing (NLP) techniques and manual curation. Here we introduce the current status of our analyses and the web database, PODC (Plant Omics Data Center; http://bioinf.mind.meiji.ac.jp/podc/), now open to the public, providing GENs, functional annotations and additional comprehensive omics resources.

KEYWORDS:

Correspondence analysis; Database; Gene expression network; Manual curation; Natural language processing (NLP); Omics

PMID:
25505034
PMCID:
PMC4301748
DOI:
10.1093/pcp/pcu188
[Indexed for MEDLINE]
Free PMC Article

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