BarleyBase
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BarleyBase is a public data resource of Affymetrix GeneChip data for plants.
Description
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BarleyBase is a public data resource of Affymetrix GeneChip data for plants.
metasource: Fairsharing.orgversion: None
BarleyBase (http://www.BarleyBase.org) is an online database for plant microarrays with integrated tools for data visualization and statistical analysis. It currently houses both raw and normalized expression data for over 1,000 hybridizations from the Affymetrix Barley1 GeneChip, and Arabidopsis ATH1 and AG genome arrays. BarleyBase is evolving to Plant Expression Database (PLEXdb) by supporting the emerging Affymetrix wheat, maize, soybean, rice and grape arrays, as well as spotted 20k rice and 58k maize long-oligo microarrays. BarleyBase supports data query, retrieval and display at all data levels, ranging from experiments to hybridizations to probe sets down to individual probes. Users can perform cross-platform and cross-experiment queries on probe sets based on expression profiles and/or on known biological annotation. Probe set queries are integrated with visualization and analysis tools such as the R/Bioconductor packages, data filters, and a large variety of plot types. BarleyBase provides integrated web-based service for functional interpretation of large scale gene expression data. Multiple gene lists can be classified, compared and visualized according to functional annotations. The gene function information includes gene ontology, Interpro protein functional domain prediction, metabolic pathway and gene family information. Controlled Plant Ontology and Gene Ontology vocabularies facilitate comparative genomic analysis through interconnecting links to PlantGDB (http://www.plantgdb.org/), Gramene (http://gramene.org/), and GrainGenes (http://wheat.pw.usda.gov/index.shtml) for sequence alignment and function prediction using BarleyBase microarray sequences.
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
Webpage:
http://barleybase.orgWebpage
More detailed information about this field from each metasource.
http://barleybase.org
metasource: Fairsharing.orgversion: None
http://www.barleybase.org/
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
Publications:
Publications
More detailed information about this field from each metasource.
BarleyBase--an expression profiling database for plant genomics
PMID: 15608273
metasource: Fairsharing.org
version: None
Publications
More detailed information about this field from each metasource.
BarleyBase--an expression profiling database for plant genomics
PMID: 15608273
metasource: Fairsharing.org
version: None
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BarleyBase--an expression profiling database for plant genomics
PubMed citations: 37.
37 articles citing: BarleyBase--an expression profiling database for plant genomics
PLEXdb: gene expression resources for plants and plant pathogens. PMID:22084198
Developmental pattern of aquaporin expression in barley (Hordeum vulgare L.) leaves. PMID:21737414
Global landscape of a co-expressed gene network in barley and its application to gene discovery in Triticeae crops. PMID:21441235
Drought response in the spikes of barley: gene expression in the lemma, palea, awn, and seed. PMID:19936810
Web-queryable large-scale data sets for hypothesis generation in plant biology. PMID:19401381
Using metabolomics to estimate unintended effects in transgenic crop plants: problems, promises, and opportunities. PMID:19137102
Towards systems genetic analyses in barley: Integration of phenotypic, expression and genotype data into GeneNetwork. PMID:19017390
Blufensin1 negatively impacts basal defense in response to barley powdery mildew. PMID:19005086
Regulon organization of Arabidopsis. PMID:18826618
OmicsViz: Cytoscape plug-in for visualizing omics data across species. PMID:18779234
Transcriptome analysis of high-temperature adult-plant resistance conditioned by Yr39 during the wheat-Puccinia striiformis f. sp. tritici interaction. PMID:18705862
Transcriptome analysis of the wheat-Puccinia striiformis f. sp. tritici interaction. PMID:18705849
Articulation of three core metabolic processes in Arabidopsis: fatty acid biosynthesis, leucine catabolism and starch metabolism. PMID:18616834
Bioinformatic tools for inferring functional information from plant microarray data II: Analysis beyond single gene. PMID:18615189
ArrayWiki: an enabling technology for sharing public microarray data repositories and meta-analyses. PMID:18541053
Bioinformatic tools for inferring functional information from plant microarray data: tools for the first steps. PMID:18528524
GeneCAT--novel webtools that combine BLAST and co-expression analyses. PMID:18480120
Surveying expression level polymorphism and single-feature polymorphism in near-isogenic wheat lines differing for the Yr5 stripe rust resistance locus. PMID:18470504
Phylogenetic and comparative gene expression analysis of barley (Hordeum vulgare) WRKY transcription factor family reveals putatively retained functions between monocots and dicots. PMID:18442363
Diversification of Lrk/Tak kinase gene clusters is associated with subfunctionalization and cultivar-specific transcript accumulation in barley. PMID:18414912
Barley genomics: An overview. PMID:18382615
Parallel expression profiling of barley-stem rust interactions. PMID:18196301
PlantTribes: a gene and gene family resource for comparative genomics in plants. PMID:18073194
PlantGDB: a resource for comparative plant genomics. PMID:18063570
Transcriptomic and metabolite analyses of Cabernet Sauvignon grape berry development. PMID:18034876
CATdb: a public access to Arabidopsis transcriptome data from the URGV-CATMA platform. PMID:17940091
Optimising the analysis of transcript data using high density oligonucleotide arrays and genomic DNA-based probe selection. PMID:17908303
Cloning and expression analysis of candidate genes involved in wax deposition along the growing barley (Hordeum vulgare) leaf. PMID:17661078
Transcript abundance profiles reveal larger and more complex responses of grapevine to chilling compared to osmotic and salinity stress. PMID:17578611
SFP genotyping from affymetrix arrays is robust but largely detects cis-acting expression regulators. PMID:17409081
A combined strategy of "in silico" transcriptome analysis and web search engine optimization allows an agile identification of reference genes suitable for normalization in gene expression studies. PMID:17143578
The plant structure ontology, a unified vocabulary of anatomy and morphology of a flowering plant. PMID:17142475
Genevestigator. Facilitating web-based gene-expression analysis. PMID:16896229
An atlas of gene expression from seed to seed through barley development. PMID:16547597
Tomato Expression Database (TED): a suite of data presentation and analysis tools. PMID:16381976
Gramene: a bird's eye view of cereal genomes. PMID:16381966
Genome-wide identification and testing of superior reference genes for transcript normalization in Arabidopsis. PMID:16166256
Tags:
Tags
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chromatin immunoprecipitation - dna microarray
metasource: Fairsharing.org
version: None
dna microarray
metasource: Fairsharing.org
version: None
microarray data and other gene expression databases
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
plant databases
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
general plant databases
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
Tags
More detailed information about this field from each metasource.
chromatin immunoprecipitation - dna microarray
metasource: Fairsharing.orgversion: None
dna microarray
metasource: Fairsharing.orgversion: None
microarray data and other gene expression databases
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
plant databases
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
general plant databases
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
chromatin immunoprecipitation - dna microarray dna microarray microarray data and other gene expression plant plant
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