ArticleDatabase : the journal of biological databases and curation2010
AthaMap-assisted transcription factor target gene identification in Arabidopsis thaliana.
Article in Database : the journal of biological databases and curation, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed, 31 citations in OpenAlex.
- Article
- TinkeringInternational journal of molecular sciences · 2020Article
- Article
- Differential Coexpression Analysis Reveals Extensive Rewiring of Arabidopsis Gene Coexpression in Response to Pseudomonas syringae Infection.Scientific reports · 2016Article
- Review
- Soybean (Glycine max) SWEET gene family: insights through comparative genomics, transcriptome profiling and whole genome re-sequence analysis.BMC genomics · 2015Article
- Expression-based network biology identifies immune-related functional modules involved in plant defense.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
- Integration of bioinformatics and synthetic promoters leads to the discovery of novel elicitor-responsive cis-regulatory sequences in Arabidopsis.Plant physiology · 2012Article
- 'MicroRNA Targets', a new AthaMap web-tool for genome-wide identification of miRNA targets in Arabidopsis thaliana.BioData mining · 2012Article
- Simple database to select promoters for plant transgenesis.Transgenic research · 2012Article
- AtPAN: an integrated system for reconstructing transcriptional regulatory networks in Arabidopsis thaliana.BMC genomics · 2012Article
- Known and novel post-transcriptional regulatory sequences are conserved across plant families.RNA (New York, N.Y.) · 2012Article
- Dynamic deposition of histone variant H3.3 accompanies developmental remodeling of the Arabidopsis transcriptome.PLoS genetics · 2012Article
- A transcriptional dynamic network during Arabidopsis thaliana pollen development.BMC systems biology · 2011Article
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The AthaMap database generates a map of potential transcription factor binding sites (TFBS) and small RNA target sites in the Arabidopsis thaliana genome. The database contains sites for 115 different transcription factors (TFs). TFBS were identified with positional weight matrices (PWMs) or with single binding sites. With the new web tool 'Gene Identification', it is possible to identify potential target genes for selected TFs. For these analyses, the user can define a region of interest of up to 6000 bp in all annotated genes. For TFBS determined with PWMs, the search can be restricted to high-quality TFBS. The results are displayed in tables that identify the gene, position of the TFBS and, if applicable, individual score of the TFBS. In addition, data files can be downloaded that harbour positional information of TFBS of all TFs in a region between -2000 and +2000 bp relative to the transcription or translation start site. Also, data content of AthaMap was increased and the database was updated to the TAIR8 genome release. Database URL: http://www.athamap.de/gene_ident.php.
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