Lotus Base: An integrated information portal for the model legume Lotus japonicus

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Lotus Base : An integrated information portal for the model legume Lotus japonicus. / Mun, Terry; Bachmann, Asger; Gupta, Vikas; Stougaard, Jens; Andersen, Stig Uggerhøj.

I: Scientific Reports, Bind 6, 39447, 23.12.2016.

Publikation: Bidrag til tidsskrift/Konferencebidrag i tidsskrift /Bidrag til avisTidsskriftartikelForskningpeer review

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@article{f774ce47451f4472acf7ba1d5c29a7a4,
title = "Lotus Base: An integrated information portal for the model legume Lotus japonicus",
abstract = "Lotus japonicus is a well-characterized model legume widely used in the study of plant-microbe interactions. However, datasets from various Lotus studies are poorly integrated and lack interoperability. We recognize the need for a comprehensive repository that allows comprehensive and dynamic exploration of Lotus genomic and transcriptomic data. Equally important are user-friendly in-browser tools designed for data visualization and interpretation. Here, we present Lotus Base, which opens to the research community a large, established LORE1 insertion mutant population containing an excess of 120,000 lines, and serves the end-user tightly integrated data from Lotus, such as the reference genome, annotated proteins, and expression profiling data. We report the integration of expression data from the L. japonicus gene expression atlas project, and the development of tools to cluster and export such data, allowing users to construct, visualize, and annotate co-expression gene networks. Lotus Base takes advantage of modern advances in browser technology to deliver powerful data interpretation for biologists. Its modular construction and publicly available application programming interface enable developers to tap into the wealth of integrated Lotus data. Lotus Base is freely accessible at: https://lotus.au.dk.",
keywords = "Bioinformatics, Data Mining, insertion mutagenesis, LORE1, Lotus japonicus, Gene expression profile, Co-expression network, Molecular Biology, Plant biology, Database, Web technology",
author = "Terry Mun and Asger Bachmann and Vikas Gupta and Jens Stougaard and Andersen, {Stig Uggerh{\o}j}",
year = "2016",
month = dec,
day = "23",
doi = "10.1038/srep39447",
language = "English",
volume = "6",
journal = "Scientific Reports",
issn = "2045-2322",
publisher = "Nature Publishing Group",

}

RIS

TY - JOUR

T1 - Lotus Base

T2 - An integrated information portal for the model legume Lotus japonicus

AU - Mun, Terry

AU - Bachmann, Asger

AU - Gupta, Vikas

AU - Stougaard, Jens

AU - Andersen, Stig Uggerhøj

PY - 2016/12/23

Y1 - 2016/12/23

N2 - Lotus japonicus is a well-characterized model legume widely used in the study of plant-microbe interactions. However, datasets from various Lotus studies are poorly integrated and lack interoperability. We recognize the need for a comprehensive repository that allows comprehensive and dynamic exploration of Lotus genomic and transcriptomic data. Equally important are user-friendly in-browser tools designed for data visualization and interpretation. Here, we present Lotus Base, which opens to the research community a large, established LORE1 insertion mutant population containing an excess of 120,000 lines, and serves the end-user tightly integrated data from Lotus, such as the reference genome, annotated proteins, and expression profiling data. We report the integration of expression data from the L. japonicus gene expression atlas project, and the development of tools to cluster and export such data, allowing users to construct, visualize, and annotate co-expression gene networks. Lotus Base takes advantage of modern advances in browser technology to deliver powerful data interpretation for biologists. Its modular construction and publicly available application programming interface enable developers to tap into the wealth of integrated Lotus data. Lotus Base is freely accessible at: https://lotus.au.dk.

AB - Lotus japonicus is a well-characterized model legume widely used in the study of plant-microbe interactions. However, datasets from various Lotus studies are poorly integrated and lack interoperability. We recognize the need for a comprehensive repository that allows comprehensive and dynamic exploration of Lotus genomic and transcriptomic data. Equally important are user-friendly in-browser tools designed for data visualization and interpretation. Here, we present Lotus Base, which opens to the research community a large, established LORE1 insertion mutant population containing an excess of 120,000 lines, and serves the end-user tightly integrated data from Lotus, such as the reference genome, annotated proteins, and expression profiling data. We report the integration of expression data from the L. japonicus gene expression atlas project, and the development of tools to cluster and export such data, allowing users to construct, visualize, and annotate co-expression gene networks. Lotus Base takes advantage of modern advances in browser technology to deliver powerful data interpretation for biologists. Its modular construction and publicly available application programming interface enable developers to tap into the wealth of integrated Lotus data. Lotus Base is freely accessible at: https://lotus.au.dk.

KW - Bioinformatics

KW - Data Mining

KW - insertion mutagenesis

KW - LORE1

KW - Lotus japonicus

KW - Gene expression profile

KW - Co-expression network

KW - Molecular Biology

KW - Plant biology

KW - Database

KW - Web technology

U2 - 10.1038/srep39447

DO - 10.1038/srep39447

M3 - Journal article

C2 - 28008948

VL - 6

JO - Scientific Reports

JF - Scientific Reports

SN - 2045-2322

M1 - 39447

ER -