Plant MicroRNA Database (PMRD)
The database integrates available plant miRNA data deposited in public databases, gleaned from the recent literature, and data generated in-house. This database contains sequence information, secondary structure, target genes, expression profiles and a genome browser. Includes model plants and major crops such as Arabidopsis, rice, wheat, soybean, maize, sorghum, barley, etc.
Description
More detailed information about this field from each metasource.
The database integrates available plant miRNA data deposited in public databases, gleaned from the recent literature, and data generated in-house. This database contains sequence information, secondary structure, target genes, expression profiles and a genome browser. Includes model plants and major crops such as Arabidopsis, rice, wheat, soybean, maize, sorghum, barley, etc.
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:35:58.540987
Webpage:
http://bioinformatics.cau.edu.cn/PMRDWebpage
More detailed information about this field from each metasource.
http://bioinformatics.cau.edu.cn/PMRD
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:35:58.540987
Publications:
Publications
More detailed information about this field from each metasource.
PMRD: plant microRNA database
PMID: 19808935
metasource: bio.tools
version: extracted_at: 2022-11-04T11:35:58.540987
Publications
More detailed information about this field from each metasource.
PMRD: plant microRNA database
PMID: 19808935
metasource: bio.tools
version: extracted_at: 2022-11-04T11:35:58.540987
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PMRD: plant microRNA database
PubMed citations: 131.
131 articles citing: PMRD: plant microRNA database
ASRmiRNA: Abiotic Stress-Responsive miRNA Prediction in Plants by Using Machine Learning Algorithms with Pseudo K-Tuple Nucleotide Compositional Features. PMID:35163534
RAD gene family analysis in cotton provides some key genes for flowering and stress tolerance in upland cotton G. hirsutum. PMID:35012446
MicroRNA-mediated bioengineering for climate-resilience in crops. PMID:34747296
Biomolecule and Bioentity Interaction Databases in Systems Biology: A Comprehensive Review. PMID:34439912
MicroRNA Databases and Tools. PMID:34432277
Genome-Wide Analysis of Coding and Non-coding RNA Reveals a Conserved miR164-NAC-mRNA Regulatory Pathway for Disease Defense in Populus. PMID:34122520
Onion (Allium cepa L.)-Derived Nanoparticles Inhibited LPS-Induced Nitrate Production, However, Their Intracellular Incorporation by Endocytosis Was Not Involved in This Effect on RAW264 Cells. PMID:34067155
Interplay between miRNAs and lncRNAs: Mode of action and biological roles in plant development and stress adaptation. PMID:34025943
Uptake of MicroRNAs from Exosome-Like Nanovesicles of Edible Plant Juice by Rat Enterocytes. PMID:33916868
MicroRNAs: Potential Targets for Developing Stress-Tolerant Crops. PMID:33800690
Dicer-like proteins influence Arabidopsis root microbiota independent of RNA-directed DNA methylation. PMID:33637135
Analysis of Rice Transcriptome Reveals the LncRNA/CircRNA Regulation in Tissue Development. PMID:33507446
Genome-wide analysis of PHD finger gene family and identification of potential miRNA and their PHD finger gene specific targets in Oryza sativa indica. PMID:33163736
Genome-wide analysis of long non-coding RNAs responsive to multiple nutrient stresses in Arabidopsis thaliana. PMID:33130916
In silico identification and validation of miRNA and their DIR specific targets in Oryza sativa Indica under abiotic stress. PMID:33024905
Discovery and validation of candidate genes for grain iron and zinc metabolism in pearl millet [Pennisetum glaucum (L.) R. Br.]. PMID:33024155
iMDA-BN: Identification of miRNA-disease associations based on the biological network and graph embedding algorithm. PMID:33005302
Delineating effect of corn microRNAs and matrix, ingested as whole food, on gut microbiota in a rodent model. PMID:32884688
A Brief Survey for MicroRNA Precursor Identification Using Machine Learning Methods. PMID:32655294
GreenCircRNA: a database for plant circRNAs that act as miRNA decoys. PMID:32510565
Development of a sensitive primer extension method for direct detection and quantification of miRNAs from plants. PMID:32163493
Comprehensive analysis of the Gossypium hirsutum L. respiratory burst oxidase homolog (Ghrboh) gene family. PMID:31996127
Identification and Characterization of circRNAs Responsive to Methyl Jasmonate in Arabidopsis thaliana. PMID:31991793
PmiREN: a comprehensive encyclopedia of plant miRNAs. PMID:31602478
MepmiRDB: a medicinal plant microRNA database. PMID:31231773
Inverse Correlation Between MPSR1 E3 Ubiquitin Ligase and HSP90.1 Balances Cytoplasmic Protein Quality Control. PMID:30890661
Plant IsomiR Atlas: Large Scale Detection, Profiling, and Target Repertoire of IsomiRs in Plants. PMID:30723486
Diff isomiRs: Large-scale detection of differential isomiRs for understanding non-coding regulated stress omics in plants. PMID:30723229
miRNomes involved in imparting thermotolerance to crop plants. PMID:30498670
Multiple Regression Analysis Reveals MicroRNA Regulatory Networks in Oryza sativa under Drought Stress. PMID:30402456
Genome-wide profiling of sRNAs in the Verticillium dahliae-infected Arabidopsis roots. PMID:30181922
A comprehensive review of web-based resources of non-coding RNAs for plant science research. PMID:29989090
ARMOUR - A Rice miRNA: mRNA Interaction Resource. PMID:29868062
Integration of the Pokeweed miRNA and mRNA Transcriptomes Reveals Targeting of Jasmonic Acid-Responsive Genes. PMID:29774043
Alternative miRNAs? Human sequences misidentified as plant miRNAs in plant studies and in human plasma. PMID:29744036
miRwayDB: a database for experimentally validated microRNA-pathway associations in pathophysiological conditions. PMID:29688364
Deciphering microRNAs and Their Associated Hairpin Precursors in a Non-Model Plant, Abelmoschus esculentus. PMID:29657290
NetMiner-an ensemble pipeline for building genome-wide and high-quality gene co-expression network using massive-scale RNA-seq samples. PMID:29425247
Overexpression of ghr-miR166b generates resistance against Bemisia tabaci infestation in Gossypium hirsutum plants. PMID:29397416
Characterization of the late embryogenesis abundant (LEA) proteins family and their role in drought stress tolerance in upland cotton. PMID:29334890
Genome-Wide Development of MicroRNA-Based SSR Markers in Medicago truncatula with Their Transferability Analysis and Utilization in Related Legume Species. PMID:29156589
A novel miRNA analysis framework to analyze differential biological networks. PMID:29097749
Non-coding RNAs and Their Roles in Stress Response in Plants. PMID:29017967
Molecular characterization of the 14-3-3 gene family in rice and its expression studies under abiotic stress. PMID:28956163
Loss of function of Arabidopsis microRNA-machinery genes impairs fertility, and has effects on homologous recombination and meiotic chromatin dynamics. PMID:28839139
Low genetic diversity and functional constraint of miRNA genes participating pollen-pistil interaction in rice. PMID:28735504
Identification and Characterization of miRNA Transcriptome in Asiatic Cotton (Gossypium arboreum) Using High Throughput Sequencing. PMID:28663752
Genome-wide characterization and expression analyses of superoxide dismutase (SOD) genes in Gossypium hirsutum. PMID:28499417
Systems biology study of transcriptional and post-transcriptional co-regulatory network sheds light on key regulators involved in important biological processes in Citrus sinensis. PMID:28461722
microRNAs as reference genes for quantitative PCR in cotton. PMID:28414734
Functional Roles of microRNAs in Agronomically Important Plants-Potential as Targets for Crop Improvement and Protection. PMID:28382044
Plant miRNAs found in human circulating system provide evidences of cross kingdom RNAi. PMID:28361700
A Comprehensive Prescription for Plant miRNA Identification. PMID:28174574
RiceATM: a platform for identifying the association between rice agronomic traits and miRNA expression. PMID:28025342
Time-Course Small RNA Profiling Reveals Rice miRNAs and Their Target Genes in Response to Rice Stripe Virus Infection. PMID:27626631
Circulating plant miRNAs can regulate human gene expression in vitro. PMID:27604570
miRNA: A Novel Link Between Rice Ragged Stunt Virus and Oryza sativa. PMID:27570315
Role of plant MicroRNA in cross-species regulatory networks of humans. PMID:27502923
MicroRNAs As Potential Targets for Abiotic Stress Tolerance in Plants. PMID:27379117
Expression Profiles, Characterization and Function of HbTCTP in Rubber Tree (Hevea brasiliensis). PMID:27375647
The impact of feature selection on one and two-class classification performance for plant microRNAs. PMID:27366641
SorghumFDB: sorghum functional genomics database with multidimensional network analysis. PMID:27352859
Feature Selection Has a Large Impact on One-Class Classification Accuracy for MicroRNAs in Plants. PMID:27190509
Deep-sequence profiling of miRNAs and their target prediction in Monotropa hypopitys. PMID:27097902
PmiRExAt: plant miRNA expression atlas database and web applications. PMID:27081157
One Step Forward, Two Steps Back; Xeno-MicroRNAs Reported in Breast Milk Are Artifacts. PMID:26824347
Identification and Expression Analyses of miRNAs from Two Contrasting Flower Color Cultivars of Canna by Deep Sequencing. PMID:26799570
Functional analysis of the Arabidopsis thaliana MUTE promoter reveals a regulatory region sufficient for stomatal-lineage expression. PMID:26748914
Role of bioinformatics in establishing microRNAs as modulators of abiotic stress responses: the new revolution. PMID:26578966
Motif content comparison between monocot and dicot species. PMID:26484161
Promoter methylation regulates the abundance of osa-miR393a in contrasting rice genotypes under salinity stress. PMID:26319531
Comprehensive meta-analysis, co-expression, and miRNA nested network analysis identifies gene candidates in citrus against Huanglongbing disease. PMID:26215595
Transcripts and MicroRNAs Responding to Salt Stress in Musa acuminata Colla (AAA Group) cv. Berangan Roots. PMID:25993649
Identification of MicroRNAs and their Targets Associated with Embryo Abortion during Chrysanthemum Cross Breeding via High-Throughput Sequencing. PMID:25909659
An integrative approach to identify hexaploid wheat miRNAome associated with development and tolerance to abiotic stress. PMID:25903161
Lipopolysaccharide perception leads to dynamic alterations in the microtranscriptome of Arabidopsis thaliana cells and leaf tissues. PMID:25848807
Identification of microRNAs and transcript targets in Camelina sativa by deep sequencing and computational methods. PMID:25826400
The liverwort Pellia endiviifolia shares microtranscriptomic traits that are common to green algae and land plants. PMID:25530158
Regulation of MAP kinase signaling cascade by microRNAs in Oryza sativa. PMID:25482813
PNRD: a plant non-coding RNA database. PMID:25398903
VIRmiRNA: a comprehensive resource for experimentally validated viral miRNAs and their targets. PMID:25380780
Identification and characterization of cold-responsive microRNAs in tea plant (Camellia sinensis) and their targets using high-throughput sequencing and degradome analysis. PMID:25330732
Integrated analysis of miRNA and mRNA expression profiles in response to Cd exposure in rice seedlings. PMID:25273267
Construction and analysis of microRNA-transcription factor regulation network in Arabidopsis. PMID:25014374
Inference of transcriptional networks in Arabidopsis through conserved noncoding sequence analysis. PMID:24989046
In silico prediction of cotton (Gossypium hirsutum) encoded microRNAs targets in the genome of Cotton leaf curl Allahabad virus. PMID:24966530
In silico identification of plant miRNAs in mammalian breast milk exosomes--a small step forward? PMID:24933019
Dual RNA-seq transcriptional analysis of wheat roots colonized by Azospirillum brasilense reveals up-regulation of nutrient acquisition and cell cycle genes. PMID:24886190
Whole-genome discovery of miRNAs and their targets in wheat (Triticum aestivum L.). PMID:24885911
SFGD: a comprehensive platform for mining functional information from soybean transcriptome data and its use in identifying acyl-lipid metabolism pathways. PMID:24712981
Next Generation Sequencing of miRNAs - Strategies, Resources and Methods. PMID:24710011
The most deeply conserved noncoding sequences in plants serve similar functions to those in vertebrates despite large differences in evolutionary rates. PMID:24681619
Identification of novel and conserved miRNAs involved in pollen development in Brassica campestris ssp. chinensis by high-throughput sequencing and degradome analysis. PMID:24559317
Computational developments in microRNA-regulated protein-protein interactions. PMID:24507415
High-throughput sequencing identification of novel and conserved miRNAs in the Brassica oleracea leaves. PMID:24245539
miRNEST 2.0: a database of plant and animal microRNAs. PMID:24243848
Machine learning approaches distinguish multiple stress conditions using stress-responsive genes and identify candidate genes for broad resistance in rice. PMID:24235132
Transcriptome sequencing and microarray design for functional genomics in the extremophile Arabidopsis relative Thellungiella salsuginea (Eutrema salsugineum). PMID:24228715
"A draft Musa balbisiana genome sequence for molecular genetics in polyploid, inter- and intra-specific Musa hybrids". PMID:24094114
A global profiling of uncapped mRNAs under cold stress reveals specific decay patterns and endonucleolytic cleavages in Brachypodium distachyon. PMID:24000894
Computational identification of conserved microRNAs and their putative targets in the Hypericum perforatum L. flower transcriptome. PMID:23846415
PMTED: a plant microRNA target expression database. PMID:23725466
Current challenges and future potential of tomato breeding using omics approaches. PMID:23641179
PlantGSEA: a gene set enrichment analysis toolkit for plant community. PMID:23632162
MicroRNAs play critical roles during plant development and in response to abiotic stresses. PMID:23412556
Genomewide analysis of intronic microRNAs in rice and Arabidopsis. PMID:23271017
Genome-wide identification of miRNAs responsive to drought in peach (Prunus persica) by high-throughput deep sequencing. PMID:23227166
Finding microRNA targets in plants: current status and perspectives. PMID:23200136
MiRGator v3.0: a microRNA portal for deep sequencing, expression profiling and mRNA targeting. PMID:23193297
The Rice Genome Knowledgebase (RGKbase): an annotation database for rice comparative genomics and evolutionary biology. PMID:23193278
Small RNA and transcriptome deep sequencing proffers insight into floral gene regulation in Rosa cultivars. PMID:23171001
Bioinformatic analysis of epigenetic and microRNA mediated regulation of drought responsive genes in rice. PMID:23145152
Computational analysis and characterization of UCE-like elements (ULEs) in plant genomes. PMID:22987666
Global alteration of microRNAs and transposon-derived small RNAs in cotton (Gossypium hirsutum) during Cotton leafroll dwarf polerovirus (CLRDV) infection. PMID:22987114
'MicroRNA Targets', a new AthaMap web-tool for genome-wide identification of miRNA targets in Arabidopsis thaliana. PMID:22800758
miRFANs: an integrated database for Arabidopsis thaliana microRNA function annotations. PMID:22583976
Genome organization and characteristics of soybean microRNAs. PMID:22559273
Next generation sequencing for profiling expression of miRNAs: technical progress and applications in drug development. PMID:22457835
AlgaGEM--a genome-scale metabolic reconstruction of algae based on the Chlamydomonas reinhardtii genome. PMID:22369158
Transgene silencing and transgene-derived siRNA production in tobacco plants homozygous for an introduced AtMYB90 construct. PMID:22363419
Bioinformatic identification of cassava miRNAs differentially expressed in response to infection by Xanthomonas axonopodis pv. manihotis. PMID:22361011
Identification of novel microRNAs in Hevea brasiliensis and computational prediction of their targets. PMID:22330773
miRNEST database: an integrative approach in microRNA search and annotation. PMID:22135287
Analysis of conserved microRNAs in floral tissues of sexual and apomictic Boechera species. PMID:21988906
Boron-dependent degradation of NIP5;1 mRNA for acclimation to excess boron conditions in Arabidopsis. PMID:21908722
ETOILE regulates developmental patterning in the filamentous brown alga Ectocarpus siliculosus. PMID:21478443
Characterization of statistical features for plant microRNA prediction. PMID:21324149
PmiRKB: a plant microRNA knowledge base. PMID:20719744
Plant microRNAs and their role in defense against viruses: a bioinformatics approach. PMID:20594353
A nematode demographics assay in transgenic roots reveals no significant impacts of the Rhg1 locus LRR-Kinase on soybean cyst nematode resistance. PMID:20529370
Genomics and bioinformatics resources for crop improvement. PMID:20208064
Tags:
Tags
More detailed information about this field from each metasource.
functional, regulatory and non-coding rna
metasource: bio.tools
version: extracted_at: 2022-11-04T11:35:58.540987
plant biology
metasource: bio.tools
version: extracted_at: 2022-11-04T11:35:58.540987
microarray experiment
metasource: bio.tools
version: extracted_at: 2022-11-04T11:35:58.540987
gene expression
metasource: bio.tools
version: extracted_at: 2022-11-04T11:35:58.540987
Tags
More detailed information about this field from each metasource.
functional, regulatory and non-coding rna
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:35:58.540987
plant biology
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:35:58.540987
microarray experiment
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:35:58.540987
gene expression
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:35:58.540987
functional, regulatory and non-coding rna plant biology microarray experiment gene expression
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