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Links tagged with 'plant gene expression regulation'

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AGRISDatabase Content

http://arabidopsis.med.ohio-state.edu/

Model Organisms > Databases

The Arabidopsis Gene Regulatory Information Server (AGRIS) provides a comprehensive resource for gene regulatory studies in the model plant Arabidopsis thaliana. Three interlinked databases, AtTFDB, AtcisDB and AtRegNet, furnish comprehensive and updated information on transcription factors (TFs), predicted and experimentally verified cis-regulatory elements (CREs) and their interactions, respectively.

NAR Database Issue 2011
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tagsarabidopsis gene regulatory networks genetic databases genetic promoter regions plant gene expression regulation transcription factors

AthaMapDatabase Content

http://www.athamap.de/

Expression > Gene Regulation
Model Organisms > Plants

AthaMap is a genome-wide map of putative transcription factor binding sites in Arabidopsis thaliana

This content is being maintained by Reinhard Hehl.

NAR Web Server Issue 2005
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tagsarabidopsis arabidopsis proteins base sequence binding sites cold temperature computational biology conserved sequence dehydration genetic databases genetic transcription genomics molecular sequence data nucleic acid databases plant dna plant gene expression regulation plant genes plant genome protein binding response elements sequence alignment systems integration transcription factors transcriptional regulatory elements untranslated rna

Plant MicroRNA DatabaseDatabase Content

http://bioinformatics.cau.edu.cn/PMRD

Model Organisms > Databases

The plant miRNA database (PMRD) 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. For Arabidopsis, rice, poplar, soybean, cotton, medicago and maize, the possible target genes for each miRNA with a predicted interaction site are included in the database. In some instances, miRNA expression profiles are included in the PMRD.

NAR Database Issue 2010
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tagscomputational biology gene expression profiling genetic databases micrornas nucleic acid databases plant gene expression regulation plant genome plants protein databases species specificity tertiary protein structure

PlnTFDBDatabase Content

http://plntfdb.bio.uni-potsdam.de/v3.0/

Expression > Gene Regulation
Model Organisms > Plants

Plant Transcription Factor Database (PlantTFDB) is database that attempts to identify a comprehensive set of plant genes coding for transcription factors. A web interface to the database allows users to browse by species, search using a sequence identifier, or query using BLAST.

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tagscomputational biology gene regulatory networks genetic databases genetic promoter regions plant diseases plant gene expression regulation plant genes plant genome plant proteins plants protein databases sequence alignment tertiary protein structure transcription factors

PlnTFDBDatabase Content

http://plntfdb.bio.uni-potsdam.de/

Model Organisms > Databases

The Plant Transcription Factor Database (PlnTFDB) is an integrative database that provides putatively complete sets of transcription factors (TFs) and other transcriptional regulators (TRs) in plant species whose genomes have been completely sequenced and annotated. For each gene family, a basic description is provided that is complemented by literature references, and multiple sequence alignments of protein domains. TF or TR gene entries include information of expressed sequence tags, 3D protein structures of homologous proteins, domain architecture and cross-links to other computational resources online. Moreover, the different species in PlnTFDB are linked to each other by means of orthologous genes facilitating cross-species comparisons.

NAR Database Issue 2010
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tagscomputational biology gene regulatory networks genetic databases plant diseases plant gene expression regulation plant genes plant genome plant proteins plants protein databases tertiary protein structure transcription factors

PREP SuiteTool Content

http://prep.unl.edu/

Model Organisms > Plants
RNA > Motifs

The PREP (Predictive RNA Editors for Plants) suite predicts sites of RNA editing based on the principle that editing in plant organelles increases the conservation of proteins across species. Predictors for mitochondrial genes, chloroplast genes, and alignments input by the user are included.

This content is being maintained by jpmower.

NAR Web Server Issue 2009
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tagsamino acid sequence amino acid sequence homology base sequence binding sites chloroplast rna chloroplasts computational biology conserved sequence cytidine dna dna sequence analysis mitochondrial genes mitochondrial proteins molecular sequence data phylogeny plant dna plant gene expression regulation plant genes plant genome plant proteins protein binding protein databases reproducibility of results rna rna editing rna sequence analysis sensitivity and specificity sequence alignment statistical models

psRNATargetTool Content

http://plantgrn.noble.org/psRNATarget/.

Model Organisms > Plants
RNA > Functional RNAs

psRNATarget is a plant small RNA target analysis server which features reverse complementary matching between small RNA and target transcript, and target site accessibility evaluation. It is designed for high-throughput analysis of next generation data, and outputs a comprehensive list of small RNA-target pairs.

NAR Web Server Issue 2011
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tagsmessenger rna micrornas plant gene expression regulation plant rna rna sequence analysis small interfering rna small untranslated rna

pssRNAMinerTool Content

http://bioinfo3.noble.org/pssRNAMiner/

Model Organisms > Plants
RNA > Functional RNAs

pssRNAMiner is a web server which identifies trans-acting siRNA clusters in plants, as well as their potential phase initiators. Users input a small RNA dataset and specify a transcript-genomic library for mapping.

NAR Web Server Issue 2008
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tagsgenomics micrornas plant gene expression regulation plant rna small interfering rna