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Expression Atlas update—an integrated database of gene and protein expression in humans, animals and plants
2015
Nucleic Acids Research
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Expression Atlas (http://www.ebi.ac.uk/gxa) provides information about gene and protein expression in animal and plant samples of different cell types, organism parts, developmental stages, diseases and ...
Since the last update, Atlas has grown sevenfold (1572 studies as of August 2015), and incorporates baseline expression profiles of tissues from Human Protein Atlas, GTEx and FANTOM5, and of cancer cell ...
of novel visualisation of differential expression tracks from Atlas. ...
doi:10.1093/nar/gkv1045
pmid:26481351
pmcid:PMC4702781
fatcat:ejfwhmtlcvbz3guoi6pkyacyji
Gramene 2018: unifying comparative genomics and pathway resources for plant research
2017
Nucleic Acids Research
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As a community portal, Gramene integrates best-of-class software and infrastructure components including the Ensembl genome browser, Reactome pathway browser, and Expression Atlas widgets, and undergoes ...
Specifically, it uses curated rice reference pathways to derive pathway projections for an additional 66 species based on gene orthology, and facilitates display of gene expression, genegene interactions ...
The funders had no role in study design, data analysis, or preparation of this manuscript. ...
doi:10.1093/nar/gkx1111
pmid:29165610
pmcid:PMC5753211
fatcat:bxgarlrs6rab5lwpixua6gotgq
Database Resources of the National Genomics Data Center in 2020
2019
Nucleic Acids Research
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expanding, updating and enriching its core database resources through big data integration and value-added curation. ...
Newly released resources include three human genome databases (PGG.SNV, PGG.Han and CGVD), eLMSG, EWAS Data Hub, GWAS Atlas, iSheep and PADS Arsenal. ...
ACKNOWLEDGEMENTS We thank a number of users for submitting data, sending suggestions, reporting bugs and getting involving in community curation. ...
doi:10.1093/nar/gkz913
pmid:31702008
pmcid:PMC7145560
fatcat:rx2p2whldnh5zpg2pyjs3mtaba
The 26th annual Nucleic Acids Research database issue and Molecular Biology Database Collection
2018
Nucleic Acids Research
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anatomy and gene (co-)expression with sophisticated visualization and session sharing. ...
This Issue contains two Breakthrough articles, on the Virtual Metabolic Human (VMH) database which links human and gut microbiota metabolism with diet and disease, and Vibrism DB, a database of mouse brain ...
ACKNOWLEDGEMENTS We thank Dr Martine Bernardes-Silva, especially, and the rest of the Oxford University Press team led by Joanna Ventikos and Elisabeth Waelkens for their help in compiling this issue. ...
doi:10.1093/nar/gky1267
pmid:30626175
pmcid:PMC6323895
fatcat:6ihilznuizgodfgkja5zsmy3mm
NONCODEV6: an updated database dedicated to long non-coding RNA annotation in both animals and plants
2020
Nucleic Acids Research
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NONCODEV6 is dedicated to providing the full scope of lncRNAs across plants and animals. The number of lncRNAs in NONCODEV6 has increased from 548 640 to 644 510 since the last update in 2017. ...
NONCODE (http://www.noncode.org/) is a comprehensive database of collection and annotation of noncoding RNAs, especially long non-coding RNAs (lncRNAs) in animals. ...
ACKNOWLEDGEMENTS We thank Heng Zhou for help with the server adjustment of NONCODEV6. ...
doi:10.1093/nar/gkaa1046
pmid:33196801
fatcat:odezd26zk5fjnfqonnmxlbeizi
Plant Reactome: a knowledgebase and resource for comparative pathway analysis
2019
Nucleic Acids Research
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In addition to browsing plant pathways, users can upload and analyze their omics data, such as the gene-expression data, and overlay curated or experimental gene-gene interaction data to extend pathway ...
Plant Reactome (https://plantreactome.gramene.org) is an open-source, comparative plant pathway knowledgebase of the Gramene project. ...
ACKNOWLEDGEMENTS We would like to thank the members of the Gramene project team at Cold Spring Harbor Laboratory for coordinating infrastructure management, database updates, and integration with the Ensembl ...
doi:10.1093/nar/gkz996
pmid:31680153
pmcid:PMC7145600
fatcat:ykzfjhf4hvgs7keopndswr5req
Gramene 2021: harnessing the power of comparative genomics and pathways for plant research
2020
Nucleic Acids Research
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We train plant researchers in biocuration of genes and pathways; host curated maize gene structures as tracks in the maize genome browser; and integrate curated rice genes and pathways in the Plant Reactome ...
Gramene integrates ontology-based protein structure–function annotation; information on genetic, epigenetic, expression, and phenotypic diversity; and gene functional annotations extracted from plant-focused ...
In addition, we thank CyVerse for providing a mirror Plant Reactome server under the Powered-by-CyVerse program. ...
doi:10.1093/nar/gkaa979
pmid:33170273
fatcat:atundz637bfalivwtye3vb3twe
AnimalTFDB 3.0: a comprehensive resource for annotation and prediction of animal transcription factors
2018
Nucleic Acids Research
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human TFs; (v) TF expressions in 22 animal species; (vi) a TF binding site prediction tool to identify potential binding TFs for nucleotide sequences; (vii) a separate human TF database web interface ( ...
AnimalTFDB contains 125,135 TF genes and 80,060 transcription cofactor genes from 97 animal genomes. Besides the expansion in data quantity, some new features and functions have been added. ...
ACKNOWLEDGEMENTS We would like to thank colleagues in data production and database construction in groups of Ensembl, dbSNP, TCGA, TRANSFAC, JASPAR, HOCOMOCO and hTFtarget. ...
doi:10.1093/nar/gky822
pmid:30204897
fatcat:f6xyu6w46jb7lgog5do72e3mzy
Omics databases in plant science: key to systems biology
2008
Plant Biotechnology
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Here, we review the current state of web databases and bioinformatics tools for plant biosciences and systems biology. ...
In addition, the number of web databases for molecular biology has rapidly increased, since most new projects construct and maintain new web databases for their own large-scale omics data. ...
Acknowledgements This work was supported in part by Grants-in-Aid for Special Research on Priority Areas (19043015) to KY from the Ministry of Education, Culture, Sports, Science and Technology of Japan ...
doi:10.5511/plantbiotechnology.25.413
fatcat:becq535uhrhblmxw5qe6vllcre
The Molecular Biology Database Collection: an updated compilation of biological database resources
2001
Nucleic Acids Research
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and expression data PROMISE http://bioinf.leeds.ac.uk/promise/ Prosthetic centers and metal ions in protein active sites Peptaibol ...
The Molecular Biology Database Collection is an online resource listing key databases of value to the biological community. ...
/axeldb.htm
Gene expression in Xenopus
Gene Identification and Structure
AllGenes
http://www.allgenes.org
Human and mouse gene index integrating gene,
transcript and protein annotation
Ares Lab ...
doi:10.1093/nar/29.1.1
pmid:11125037
pmcid:PMC29860
fatcat:t7pctxvehncsfliq6a4nywqx5u
Present Scenario of Long Non-Coding RNAs in Plants
2017
Non-Coding RNA
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However, the status of lncRNA investigation in plants lags behind that in animals (especially humans). ...
Since then, research in animals, particularly in humans, has rapidly progressed, and a vast amount of data has been generated, collected, and organized using computational approaches. ...
In future, development of lncRNA prediction tools (like those for animals and humans) based on data beyond sequences (like gene expression data and protein-interaction data) would further catalyze the ...
doi:10.3390/ncrna3020016
pmid:29657289
pmcid:PMC5831932
fatcat:xbdgh4afofgrvnufuw3gdgcelu
Database Resources of the BIG Data Center in 2019
2018
Nucleic Acids Research
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Newly released resources include EWAS Atlas (a knowledgebase of epigenome- wide association studies), iDog (an integrated omics data resource for dog) and RNA editing resources (for editome-disease associations ...
The BIG Data Center at Beijing Institute of Genomics (BIG) of the Chinese Academy of Sciences provides a suite of database resources in support of worldwide research activities in both academia and industry ...
The BIG Data Center is indebted to its funders, including the Ministry of Science and Technology of China, the Natural Science Foundation of China, the CAS and BIG. ...
doi:10.1093/nar/gky993
pmid:30365034
fatcat:ech7n6ssxjho5pryujoh75v2om
The Molecular Biology Database Collection: 2002 update
2002
Nucleic Acids Research
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Short, searchable summaries and updates for each of the databases included in the Collection are available through the Nucleic Acids Research Web site at http:// nar.oupjournals.org. ...
The Molecular Biology Database Collection is an online resource listing key databases of value to the biological community. ...
(MGI)
https://xgi.ncgr.org/mgi
Model legume Medicago ESTs, gene expression and
proteomic data
Mendel Database
http://www.mendel.ac.uk/
Database of plant EST and STS sequences annotated
with gene ...
doi:10.1093/nar/30.1.1
pmid:11752241
pmcid:PMC99169
fatcat:n46iu5l6oreapd5yxswe7pmg5m
A comprehensive review of web-based resources of non-coding RNAs for plant science research
2018
International Journal of Biological Sciences
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Acknowledgements The research was supported in part by two grants (No. 31460295 and 31760314) of National Natural Science Foundation of China (http://www.nsfc.gov.cn/) and a grant (No. ...
The miRNA predictions performed on Expressed Sequence Tags of 202 plant and 225 animal species are the core of this database [81] . ...
, translational gene expression, modulation of protein function and subcellular distribution of RNAs and proteins [132, 133] . ...
doi:10.7150/ijbs.24593
pmid:29989090
pmcid:PMC6036741
fatcat:ega4utdykbap5m4zgavecnprli
The 24th annualNucleic Acids Researchdatabase issue: a look back and upcoming changes
2017
Nucleic Acids Research
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As always, these databases cover a broad range of molecular biology subjects, including genome structure, gene expression and its regulation, proteins, protein domains, and proteinprotein interactions. ...
Following the recent trend, an increasing number of new and established databases deal with the issues of human health, from cancercausing mutations to drugs and drug targets. ...
Martine Bernardes-Silva and the Oxford University Press team led by Jennifer Boyd for their help in assembling this issue. ...
doi:10.1093/nar/gkw1188
pmid:28053160
pmcid:PMC5210597
fatcat:jbvd2nm6undn5k4rtwng33pxiq
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