ArticlePlant & cell physiology2013
STIFDB2: an updated version of plant stress-responsive transcription factor database with additional stress signals, stress-responsive transcription factor binding sites and stress-responsive genes in Arabidopsis and rice.
Article in Plant & cell physiology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 52 papers.
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52 citing papers in PubMed, 130 citations in OpenAlex.
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- Identification and expression analysis of candidate genes associated with stem gall disease in Coriander (Coriandrum sativum L.) cultivars.Molecular biology reports · 2020Article
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- Genome-wide identification of cold responsive transcription factors in Brassica napus L.BMC plant biology · 2020Article
- Distinct Evolutionary Origins of Intron Retention Splicing Events inFrontiers in plant science · 2020Article
- Rice Stress-Resistant SNP Database.Rice (New York, N.Y.) · 2019Article
- Genes, pathways and transcription factors involved in seedling stage chilling stress tolerance in indica rice through RNA-Seq analysis.BMC plant biology · 2019Article
- Infrastructures of systems biology that facilitate functional genomic study in rice.Rice (New York, N.Y.) · 2019Review
- The complete chloroplast genome of the threatenedJournal of genetics · 2019Article
- Comparative transcriptome analysis reveals KBMC plant biology · 2019Article
- Genome-Wide Identification of Splicing Quantitative Trait Loci (sQTLs) in Diverse Ecotypes ofFrontiers in plant science · 2019Article
- Genome-Wide Analysis of Domain-Swap Predicted Products in the Genome of Anti-Stress Medicinal Plant:Bioinformatics and biology insights · 2019Article
Corrections and comments
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Authors and funding
5 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Understanding the principles of abiotic and biotic stress responses, tolerance and adaptation remains important in plant physiology research to develop better varieties of crop plants. Better understanding of plant stress response mechanisms and application of knowledge derived from integrated experimental and bioinformatics approaches are gaining importance. Earlier, we showed that compiling a database of stress-responsive transcription factors and their corresponding target binding sites in the form of Hidden Markov models at promoter, untranslated and upstream regions of stress-up-regulated genes from expression analysis can help in elucidating various aspects of the stress response in Arabidopsis. In addition to the extensive content in the first version, STIFDB2 is now updated with 15 stress signals, 31 transcription factors and 5,984 stress-responsive genes from three species (Arabidopsis thaliana, Oryza sativa subsp. japonica and Oryza sativa subsp. indica). We have employed an integrated biocuration and genomic data mining approach to characterize the data set of transcription factors and consensus binding sites from literature mining and stress-responsive genes from the Gene Expression Omnibus. STIFDB2 currently has 38,798 associations of stress signals, stress-responsive genes and transcription factor binding sites predicted using the Stress-responsive Transcription Factor (STIF) algorithm, along with various functional annotation data. As a unique plant stress regulatory genomics data platform, STIFDB2 can be utilized for targeted as well as high-throughput experimental and computational studies to unravel principles of the stress regulome in dicots and gramineae. STIFDB2 is available from the URL: http://caps.ncbs.res.in/stifdb2.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.