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Plant Omics Data Center: An Integrated Web Repository for Interspecies Gene Expression Networks with NLP-Based Curation

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 n...

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Autores principales: Ohyanagi, Hajime, Takano, Tomoyuki, Terashima, Shin, Kobayashi, Masaaki, Kanno, Maasa, Morimoto, Kyoko, Kanegae, Hiromi, Sasaki, Yohei, Saito, Misa, Asano, Satomi, Ozaki, Soichi, Kudo, Toru, Yokoyama, Koji, Aya, Koichiro, Suwabe, Keita, Suzuki, Go, Aoki, Koh, Kubo, Yasutaka, Watanabe, Masao, Matsuoka, Makoto, Yano, Kentaro
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4301748/
https://www.ncbi.nlm.nih.gov/pubmed/25505034
http://dx.doi.org/10.1093/pcp/pcu188
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author Ohyanagi, Hajime
Takano, Tomoyuki
Terashima, Shin
Kobayashi, Masaaki
Kanno, Maasa
Morimoto, Kyoko
Kanegae, Hiromi
Sasaki, Yohei
Saito, Misa
Asano, Satomi
Ozaki, Soichi
Kudo, Toru
Yokoyama, Koji
Aya, Koichiro
Suwabe, Keita
Suzuki, Go
Aoki, Koh
Kubo, Yasutaka
Watanabe, Masao
Matsuoka, Makoto
Yano, Kentaro
author_facet Ohyanagi, Hajime
Takano, Tomoyuki
Terashima, Shin
Kobayashi, Masaaki
Kanno, Maasa
Morimoto, Kyoko
Kanegae, Hiromi
Sasaki, Yohei
Saito, Misa
Asano, Satomi
Ozaki, Soichi
Kudo, Toru
Yokoyama, Koji
Aya, Koichiro
Suwabe, Keita
Suzuki, Go
Aoki, Koh
Kubo, Yasutaka
Watanabe, Masao
Matsuoka, Makoto
Yano, Kentaro
author_sort Ohyanagi, Hajime
collection PubMed
description 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.
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spelling pubmed-43017482015-02-03 Plant Omics Data Center: An Integrated Web Repository for Interspecies Gene Expression Networks with NLP-Based Curation Ohyanagi, Hajime Takano, Tomoyuki Terashima, Shin Kobayashi, Masaaki Kanno, Maasa Morimoto, Kyoko Kanegae, Hiromi Sasaki, Yohei Saito, Misa Asano, Satomi Ozaki, Soichi Kudo, Toru Yokoyama, Koji Aya, Koichiro Suwabe, Keita Suzuki, Go Aoki, Koh Kubo, Yasutaka Watanabe, Masao Matsuoka, Makoto Yano, Kentaro Plant Cell Physiol Special Online Collection – Database Papers 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. Oxford University Press 2015-01 2014-12-11 /pmc/articles/PMC4301748/ /pubmed/25505034 http://dx.doi.org/10.1093/pcp/pcu188 Text en © The Author 2014. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Special Online Collection – Database Papers
Ohyanagi, Hajime
Takano, Tomoyuki
Terashima, Shin
Kobayashi, Masaaki
Kanno, Maasa
Morimoto, Kyoko
Kanegae, Hiromi
Sasaki, Yohei
Saito, Misa
Asano, Satomi
Ozaki, Soichi
Kudo, Toru
Yokoyama, Koji
Aya, Koichiro
Suwabe, Keita
Suzuki, Go
Aoki, Koh
Kubo, Yasutaka
Watanabe, Masao
Matsuoka, Makoto
Yano, Kentaro
Plant Omics Data Center: An Integrated Web Repository for Interspecies Gene Expression Networks with NLP-Based Curation
title Plant Omics Data Center: An Integrated Web Repository for Interspecies Gene Expression Networks with NLP-Based Curation
title_full Plant Omics Data Center: An Integrated Web Repository for Interspecies Gene Expression Networks with NLP-Based Curation
title_fullStr Plant Omics Data Center: An Integrated Web Repository for Interspecies Gene Expression Networks with NLP-Based Curation
title_full_unstemmed Plant Omics Data Center: An Integrated Web Repository for Interspecies Gene Expression Networks with NLP-Based Curation
title_short Plant Omics Data Center: An Integrated Web Repository for Interspecies Gene Expression Networks with NLP-Based Curation
title_sort plant omics data center: an integrated web repository for interspecies gene expression networks with nlp-based curation
topic Special Online Collection – Database Papers
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4301748/
https://www.ncbi.nlm.nih.gov/pubmed/25505034
http://dx.doi.org/10.1093/pcp/pcu188
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