{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,7,30]],"date-time":"2025-07-30T11:49:23Z","timestamp":1753876163922,"version":"3.41.2"},"reference-count":34,"publisher":"Oxford University Press (OUP)","license":[{"start":{"date-parts":[[2019,12,4]],"date-time":"2019-12-04T00:00:00Z","timestamp":1575417600000},"content-version":"vor","delay-in-days":337,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001412","name":"Council of Scientific and Industrial Research","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100001412","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Department of Science and Technology\/Science and Engineering Research Board"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Gene regulation is a highly complex and networked phenomenon where multiple tiers of control determine the cell state in a spatio-temporal manner. Among these, the transcription factors, DNA and histone modifications, and post-transcriptional control by small RNAs like miRNAs serve as major regulators. An understanding of the integrative and spatio-temporal impact of these regulatory factors can provide better insights into the state of a \u2018cell system\u2019. Yet, there are limited resources available to this effect. Therefore, we hereby report an integrative information portal (Plant Regulomics Portal; PRP) for plants for the first time. The portal has been developed by integrating a huge amount of curated data from published sources, RNA-, methylome- and sRNA\/miRNA sequencing, histone modifications and repeats, gene ontology, digital gene expression and characterized pathways. The key features of the portal include a regulatory search engine for fetching numerous analytical outputs and tracks of the abovementioned regulators and also a genome browser for integrated visualization of the search results. It also has numerous analytical features for analyses of transcription factors (TFs) and sRNA\/miRNA, spot-specific methylation, gene expression and interactions and details of pathways for any given genomic element. It can also provide information on potential RdDM regulation, while facilitating enrichment analysis, generation of visually rich plots and downloading of data in a selective manner. Visualization of intricate biological networks is an important feature which utilizes the Neo4j Graph database making analysis of relationships and long-range system viewing possible. Till date, PRP hosts 571-GB processed data for four plant species namely Arabidopsis thaliana, Oryza sativa subsp. japonica, Zea mays and Glycine max.<\/jats:p><jats:p>Database URL: https:\/\/scbb.ihbt.res.in\/PRP<\/jats:p>","DOI":"10.1093\/database\/baz130","type":"journal-article","created":{"date-parts":[[2019,11,2]],"date-time":"2019-11-02T12:10:54Z","timestamp":1572696654000},"source":"Crossref","is-referenced-by-count":2,"title":["Plant Regulomics Portal (PRP): a comprehensive integrated regulatory information and analysis portal for plant genomes"],"prefix":"10.1093","volume":"2019","author":[{"given":"Ganesh","family":"Panzade","sequence":"first","affiliation":[{"name":"Studio of Computational Biology & Bioinformatics, Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, Kangra, Himachal Pradesh 176061, India"},{"name":"Academy of Scientific & Innovative Research (AcSIR), CSIR-HRDC Campus, Postal Staff College Area, Sector 19, Kamla Nehru Nagar, Ghaziabad, Uttar Pradesh 201002, India"},{"name":"Division of Biology, Kansas State University, Zinovyeva Lab, 28 Ackert Hall, Manhattan, KS, USA, 66506"}]},{"given":"Indu","family":"Gangwar","sequence":"additional","affiliation":[{"name":"Studio of Computational Biology & Bioinformatics, Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, Kangra, Himachal Pradesh 176061, India"},{"name":"Academy of Scientific & Innovative Research (AcSIR), CSIR-HRDC Campus, Postal Staff College Area, Sector 19, Kamla Nehru Nagar, Ghaziabad, Uttar Pradesh 201002, India"}]},{"given":"Supriya","family":"Awasthi","sequence":"additional","affiliation":[{"name":"Studio of Computational Biology & Bioinformatics, Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, Kangra, Himachal Pradesh 176061, India"}]},{"given":"Nitesh","family":"Sharma","sequence":"additional","affiliation":[{"name":"Studio of Computational Biology & Bioinformatics, Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, Kangra, Himachal Pradesh 176061, India"},{"name":"Academy of Scientific & Innovative Research (AcSIR), CSIR-HRDC Campus, Postal Staff College Area, Sector 19, Kamla Nehru Nagar, Ghaziabad, Uttar Pradesh 201002, India"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3940-6724","authenticated-orcid":false,"given":"Ravi","family":"Shankar","sequence":"additional","affiliation":[{"name":"Studio of Computational Biology & Bioinformatics, Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, Kangra, Himachal Pradesh 176061, India"},{"name":"Academy of Scientific & Innovative Research (AcSIR), CSIR-HRDC Campus, Postal Staff College Area, Sector 19, Kamla Nehru Nagar, Ghaziabad, Uttar Pradesh 201002, India"}]}],"member":"286","published-online":{"date-parts":[[2019,12,3]]},"reference":[{"key":"2019120401104264400_ref1","doi-asserted-by":"crossref","first-page":"656","DOI":"10.1016\/j.cell.2009.01.045","article-title":"Small RNAs as guardians of the genome","volume":"136","author":"Malone","year":"2009","journal-title":"Cell"},{"key":"2019120401104264400_ref2","doi-asserted-by":"crossref","first-page":"495","DOI":"10.1139\/o11-046","article-title":"Genomic relationship between SINE retrotransposons, Pol III-Pol II transcription, and chromatin organization: the journey from junk to jewel","volume":"89","author":"Lunyak","year":"2011","journal-title":"Biochem Cell Biol."},{"key":"2019120401104264400_ref3","doi-asserted-by":"crossref","first-page":"e1000598","DOI":"10.1371\/journal.pgen.1000598","article-title":"Production and processing of siRNA precursor transcripts from the highly repetitive maize genome","volume":"5","author":"Hale","year":"2009","journal-title":"PLoS Genet."},{"key":"2019120401104264400_ref4","doi-asserted-by":"crossref","first-page":"e29255","DOI":"10.4161\/mge.29255","article-title":"Burgeoning evidence indicates that microRNAs were initially formed from transposable element sequences","volume":"4","author":"Roberts","year":"2014","journal-title":"Mob. Genet. Elements"},{"key":"2019120401104264400_ref5","doi-asserted-by":"crossref","first-page":"367","DOI":"10.1016\/j.ceb.2009.01.025","article-title":"RNA-mediated chromatin-based silencing in plants","volume":"21","author":"Matzke","year":"2009","journal-title":"Curr. Opin. Cell Biol."},{"key":"2019120401104264400_ref6","doi-asserted-by":"crossref","first-page":"4","DOI":"10.1186\/1471-2148-4-37","article-title":"Evolution and distribution of RNA polymerase II regulatory sites from RNA polymerase III dependent mobile Alu elements","volume":"4","author":"Shankar","year":"2004","journal-title":"BMC Evol. Biol."},{"key":"2019120401104264400_ref7","doi-asserted-by":"crossref","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: a flexible trimmer for Illumina sequence data","author":"Bolger","year":"2014","journal-title":"Bioinformatics"},{"key":"2019120401104264400_ref8","doi-asserted-by":"crossref","first-page":"562","DOI":"10.1038\/nprot.2012.016","article-title":"Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks","volume":"7","author":"Trapnell","year":"2012","journal-title":"Nat. Protocols"},{"issue":"6","key":"2019120401104264400_ref9","doi-asserted-by":"crossref","first-page":"740","DOI":"10.1261\/rna.035279.112","article-title":"ShortStack: comprehensive annotation and quantification of small RNA genes","volume":"19","author":"Axtell","year":"2013","journal-title":"RNA"},{"issue":"11","key":"2019120401104264400_ref10","doi-asserted-by":"crossref","first-page":"1571","DOI":"10.1093\/bioinformatics\/btr167","article-title":"Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications","volume":"27","author":"Krueger","year":"2011","journal-title":"Bioinformatics"},{"issue":"1\u20134","key":"2019120401104264400_ref11","doi-asserted-by":"crossref","first-page":"462","DOI":"10.1159\/000084979","article-title":"Repbase update, a database of eukaryotic repetitive elements","volume":"110","author":"Jurka","year":"2005","journal-title":"Cytogenet. Genome Res."},{"issue":"22","key":"2019120401104264400_ref12","doi-asserted-by":"crossref","first-page":"3593","DOI":"10.1093\/bioinformatics\/btv422","article-title":"Tetranscripts: a package for including transposable elements in differential expression analysis of RNA-seq datasets","volume":"31","author":"Jin","year":"2015","journal-title":"Bioinformatics"},{"key":"2019120401104264400_ref13","doi-asserted-by":"crossref","first-page":"636","DOI":"10.1186\/1471-2164-12-636","article-title":"Employing machine learning for reliable miRNA target identification in plants","volume":"12","author":"Jha","year":"2011","journal-title":"BMC Genomics."},{"key":"2019120401104264400_ref14","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkr319","article-title":"psRNATarget: a plant small RNA target analysis server","author":"Dai","year":"2011","journal-title":"Nucleic Acids Res."},{"issue":"1","key":"2019120401104264400_ref15","doi-asserted-by":"crossref","first-page":"130","DOI":"10.1093\/bioinformatics\/btn604","article-title":"CleaveLand: a pipeline for using degradome data to find cleaved small RNA targets","volume":"25","author":"Addo-Quaye","year":"2009","journal-title":"Bioinformatics"},{"issue":"3","key":"2019120401104264400_ref16","doi-asserted-by":"crossref","first-page":"R25","DOI":"10.1186\/gb-2009-10-3-r25","article-title":"Ultrafast and memory-efficient alignment of short DNA sequences to the human genome","volume":"10","author":"Langmead","year":"2009","journal-title":"Genome Biol."},{"issue":"4","key":"2019120401104264400_ref17","doi-asserted-by":"crossref","first-page":"514","DOI":"10.1093\/bioinformatics\/btw683","article-title":"Fast motif matching revisited: high-order PWMs, SNPs and indels","volume":"33","author":"Korhonen","year":"2017","journal-title":"Bioinformatics"},{"issue":"1","key":"2019120401104264400_ref18","doi-asserted-by":"crossref","first-page":"e12","DOI":"10.1093\/pcp\/pcv200","article-title":"HRGRN: a graph search-empowered integrative database of Arabidopsis signaling transductiion, metabolism and gene regulation networks","volume":"57","author":"Dai","year":"2016","journal-title":"Plant Cell Physiol."},{"issue":"Suppl 13","key":"2019120401104264400_ref19","doi-asserted-by":"crossref","first-page":"1027","DOI":"10.1186\/s12864-016-3326-6","article-title":"TEA: the epigenome platform for Arabidopsis methylome study","volume":"17","author":"Su","year":"2016","journal-title":"BMC Genomics."},{"key":"2019120401104264400_ref20","doi-asserted-by":"crossref","first-page":"154","DOI":"10.1038\/nbt.2462","article-title":"Single-base resolution methylomes of tomato fruit development reveal epigenome modifications associated with ripening","volume":"31","author":"Zhong","year":"2013","journal-title":"Nature Biotechnol."},{"key":"2019120401104264400_ref21","doi-asserted-by":"crossref","first-page":"118","DOI":"10.1126\/science.1106910","article-title":"RNA polymerase IV directs silencing of endogenous DNA","volume":"308","author":"Herr","year":"2005","journal-title":"Science"},{"issue":"1","key":"2019120401104264400_ref22","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/S1016-8478(23)13130-X","article-title":"Small Rnas: classification, biogenesis, and Function","volume":"19","author":"Kim","year":"2005","journal-title":"Mol. Cells"},{"issue":"5","key":"2019120401104264400_ref23","doi-asserted-by":"crossref","first-page":"613","DOI":"10.1016\/j.cell.2005.02.007","article-title":"Plant nuclear RNA polymerase IV mediates siRNA and DNA methylation-dependent heterochromatin formation","volume":"120","author":"Onodera","year":"2005","journal-title":"Cell"},{"key":"2019120401104264400_ref24","doi-asserted-by":"crossref","first-page":"1237","DOI":"10.3389\/fmicb.2015.01237","article-title":"Biogenesis, function, and applications of virus-derived small RNAs in plants","volume":"6","author":"Zhang","year":"2015","journal-title":"Front. Microbiol."},{"key":"2019120401104264400_ref25","doi-asserted-by":"crossref","first-page":"204","DOI":"10.1038\/nrg2719","article-title":"Establishing, maintaining and modifying DNA methylation patterns in plants and animals","volume":"11","author":"Law","year":"2010","journal-title":"Nat. Rev. Genet."},{"issue":"2","key":"2019120401104264400_ref26","doi-asserted-by":"crossref","first-page":"142","DOI":"10.1016\/j.pbi.2011.02.003","article-title":"RNA-directed DNA methylation","volume":"14","author":"Zhang","year":"2011","journal-title":"Curr Opin Plant Biol."},{"key":"2019120401104264400_ref27","doi-asserted-by":"crossref","DOI":"10.1186\/gb-2012-13-10-r87","article-title":"methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles","volume":"13","author":"Akalin","year":"2012","journal-title":"Genome Biol."},{"key":"2019120401104264400_ref28","doi-asserted-by":"crossref","first-page":"567","DOI":"10.1016\/0092-8674(94)90119-8","article-title":"RNA-directed de novo methylation of genomic sequences in plants","volume":"76","author":"Wassenegger","year":"1994","journal-title":"Cell"},{"key":"2019120401104264400_ref29","doi-asserted-by":"crossref","first-page":"106","DOI":"10.1038\/nature09025","article-title":"An RNA polymerase II- and AGO4-associated protein acts in RNA-directed DNA methylation","volume":"465","author":"Gao","year":"2010","journal-title":"Nature"},{"key":"2019120401104264400_ref30","first-page":"12","article-title":"Node importance measurement based on the degree and clustering coefficient information","volume":"62","author":"Ren","year":"2013","journal-title":"Acta Physica Sinica"},{"issue":"2","key":"2019120401104264400_ref31","doi-asserted-by":"crossref","first-page":"219","DOI":"10.1093\/nsr\/nwu003","article-title":"Noncoding RNAs and DNA methylation in plants","volume":"1","author":"Zhao","year":"2014","journal-title":"Natl Sci Rev."},{"issue":"2","key":"2019120401104264400_ref32","doi-asserted-by":"crossref","first-page":"1037","DOI":"10.1104\/pp.112.204263","article-title":"Putative glycosyltransferases and other Golgi apparatus proteins are revealed by LOPIT proteomics","volume":"160","author":"Nikolovski","year":"2012","journal-title":"Plant Physio."},{"issue":"2","key":"2019120401104264400_ref33","doi-asserted-by":"crossref","first-page":"281","DOI":"10.1016\/S0092-8674(04)00045-5","article-title":"Micro RNAs: genomics, biogenesis, mechanism, and function","volume":"116","author":"Bartel","year":"2004","journal-title":"Cell."},{"issue":"5651","key":"2019120401104264400_ref34","doi-asserted-by":"crossref","first-page":"1751","DOI":"10.1126\/science.1091109","article-title":"Regulation of flowering time by histone acetylation in Arabidopsis","volume":"302","author":"Hey","year":"2004","journal-title":"Science"}],"container-title":["Database"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/database\/article-pdf\/doi\/10.1093\/database\/baz130\/31193672\/baz130.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"http:\/\/academic.oup.com\/database\/article-pdf\/doi\/10.1093\/database\/baz130\/31193672\/baz130.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,7,26]],"date-time":"2024-07-26T04:23:39Z","timestamp":1721967819000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/database\/article\/doi\/10.1093\/database\/baz130\/5650983"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,1,1]]},"references-count":34,"URL":"https:\/\/doi.org\/10.1093\/database\/baz130","relation":{},"ISSN":["1758-0463"],"issn-type":[{"type":"electronic","value":"1758-0463"}],"subject":[],"published-other":{"date-parts":[[2019]]},"published":{"date-parts":[[2019,1,1]]},"article-number":"baz130"}}