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Expression Atlas update—an integrated database of gene and protein expression in humans, animals and plants

Robert Petryszak, Maria Keays, Y. Amy Tang, Nuno A. Fonseca, Elisabet Barrera, Tony Burdett, Anja Füllgrabe, Alfonso Muñoz-Pomer Fuentes, Simon Jupp, Satu Koskinen, Oliver Mannion, Laura Huerta (+12 others)
2015 Nucleic Acids Research  
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

Marcela K Tello-Ruiz, Sushma Naithani, Joshua C Stein, Parul Gupta, Michael Campbell, Andrew Olson, Sharon Wei, Justin Preece, Matthew J Geniza, Yinping Jiao, Young Koung Lee, Bo Wang (+27 others)
2017 Nucleic Acids Research  
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  
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

Daniel J Rigden, Xosé M Fernández
2018 Nucleic Acids Research  
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

Lianhe Zhao, Jiajia Wang, Yanyan Li, Tingrui Song, Yang Wu, Shuangsang Fang, Dechao Bu, Hui Li, Liang Sun, Dong Pei, Yu Zheng, Jianqin Huang (+4 others)
2020 Nucleic Acids Research  
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  
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

Marcela K Tello-Ruiz, Sushma Naithani, Parul Gupta, Andrew Olson, Sharon Wei, Justin Preece, Yinping Jiao, Bo Wang, Kapeel Chougule, Priyanka Garg, Justin Elser, Sunita Kumari (+17 others)
2020 Nucleic Acids Research  
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

Hui Hu, Ya-Ru Miao, Long-Hao Jia, Qing-Yang Yu, Qiong Zhang, An-Yuan Guo
2018 Nucleic Acids Research  
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

Keita Suwabe, Kentaro Yano
2008 Plant Biotechnology  
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

A. D. Baxevanis
2001 Nucleic Acids Research  
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

Garima Bhatia, Neetu Goyal, Shailesh Sharma, Santosh Upadhyay, Kashmir Singh
2017 Non-Coding RNA  
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

Zhang Zhang, Wenming Zhao, Jingfa Xiao, Yiming Bao, Fan Wang, Lili Hao, Junwei Zhu, Tingting Chen, Sisi Zhang, Xu Chen, Bixia Tang, Qing Zhou (+147 others)
2018 Nucleic Acids Research  
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

A. D. Baxevanis
2002 Nucleic Acids Research  
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

Peiran Liao, Shipeng Li, Xiuming Cui, Yun Zheng
2018 International Journal of Biological Sciences  
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

Michael Y. Galperin, Xosé M. Fernández-Suárez, Daniel J. Rigden
2017 Nucleic Acids Research  
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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