ArticleNucleic acids research2009
AthaMap, integrating transcriptional and post-transcriptional data.
Article in Nucleic acids research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers, 1 of them a synthesis that pooled it.
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Who cites it
32 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Comparative transcriptome meta-analysis of Arabidopsis thaliana under drought and cold stress.PloS one · 2018Pooled it
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- Genomic distribution and context dependent functionality of novel WRKY transcription factor binding sites.BMC genomics · 2022Article
- TDTHub, a web server tool for the analysis of transcription factor binding sites in plants.The Plant journal : for cell and molecular biology · 2022Article
- RSAT matrix-clustering: dynamic exploration and redundancy reduction of transcription factor binding motif collections.Nucleic acids research · 2017Article
- Article
- Cis regulatory motifs and antisense transcriptional control in the apicomplexan Theileria parva.BMC genomics · 2016Article
- An affinity-structure database of helix-turn-helix: DNA complexes with a universal coordinate system.BMC bioinformatics · 2015Article
- Nitrate sensing by the maize root apex transition zone: a merged transcriptomic and proteomic survey.Journal of experimental botany · 2015Article
- Regulatory interplay between soybean root and soybean cyst nematode during a resistant and susceptible reaction.BMC plant biology · 2014Article
- Regulatory network rewiring for secondary metabolism in Arabidopsis thaliana under various conditions.BMC plant biology · 2014Article
- Integrating bioinformatic resources to predict transcription factors interacting with cis-sequences conserved in co-regulated genes.BMC genomics · 2014Article
- Characterization of putative cis-regulatory elements in genes preferentially expressed in Arabidopsis male meiocytes.BioMed research international · 2014Article
- 'In silico expression analysis', a novel PathoPlant web tool to identify abiotic and biotic stress conditions associated with specific cis-regulatory sequences.Database : the journal of biological databases and curation · 2014Article
- Rice DB: an Oryza Information Portal linking annotation, subcellular location, function, expression, regulation, and evolutionary information for rice and Arabidopsis.The Plant journal : for cell and molecular biology · 2013Article
- Nitrogen transporter and assimilation genes exhibit developmental stage-selective expression in maize (Zea mays L.) associated with distinct cis-acting promoter motifs.Plant signaling & behavior · 2013Article
- Using an ensemble of statistical metrics to quantify large sets of plant transcription factor binding sites.Plant methods · 2013Article
- Article
- Transcriptional regulation of tocopherol biosynthesis in tomato.Plant molecular biology · 2013Article
- Molecular signatures in Arabidopsis thaliana in response to insect attack and bacterial infection.PloS one · 2013Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The AthaMap database generates a map of predicted transcription factor binding sites (TFBS) for the whole Arabidopsis thaliana genome. AthaMap has now been extended to include data on post-transcriptional regulation. A total of 403,173 genomic positions of small RNAs have been mapped in the A. thaliana genome. These identify 5772 putative post-transcriptionally regulated target genes. AthaMap tools have been modified to improve the identification of common TFBS in co-regulated genes by subtracting post-transcriptionally regulated genes from such analyses. Furthermore, AthaMap was updated to the TAIR7 genome annotation, a graphic display of gene analysis results was implemented, and the TFBS data content was increased. AthaMap is freely available at http://www.athamap.de/.
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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 OpenQuestion graph.