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Agris Website Tutorial

Tutorial Sections and Quick Links Fasta/CSV downloads
Links to download fasta or csv files appear throughout AGRIS.
  • Download gene list - download a table where each row represents a gene, similar to on-screen tables
  • Download sequences (csv) - download a table where each row contains a transcript ID and sequence
  • Download sequences (fasta) - download transcript IDs and sequences in fasta format

AtcisDB - Arabidopsis cis-regulatory element database

AtcisDB provides a comprehensive resource for the scientific community working with gene regulatory information of Arabidopsis thaliana. AtcisDB consists of a searchable relational database, which includes many different data types, such as transcription factor binding site information, promoter sequence and related annotations. The data can be viewed using the Generic Genome Browser.

AtcisDB can be searched by Gene Symbol or Locus ID. The Gene Symbol can be any symbol used by TAIR for gene annotation (e.g., NAC, CAF, MYB etc.). The Locus ID is also the ID used by TAIR (e.g,. At1g01010, At1g01050 etc.). The search results will include the Locus ID, the Gene Model that represents that locus, and cross reference for gene annotation from MIPS, TIGR, TAIR and SALK. The cis-regulatory element annotation for each gene can also be obtained.

The binding sites are color-coded with two colors: RED and GREY. The RED color indicates experimentally validated cis-regulatory element present in a specific promoter. The GREY color indicates predicted motifs. For the complete list of binding sites used in these anlayses please click here Bindingsites List.

Frequencies for words of length 5 - 15 across the non-coding segments of the Arabidopsis genome are available for download [1].

Arabidopsis core promoters were defined as the region flanking 50 bps to each side the transcription start site (TSS), in cases when TSS have been established. Click here to download Core Promoter data [2].

For details please read AtcisDB HELP.

AtTFDB - Arabidopsis transcription factor database

AtTFDB is a comprehensive and public Arabidopsis TF database. The criteria employed for TF identification was described in Davuluri et al., 2003 and Palaniswamy et al., 2006. The sequence of the TFs currently in AtTFDB corresponds to the most current release of the Arabidopsis genome in TAIR (TAIR9).

From this page, users may search the database for TFs in two ways:
a) By utilizing a specific LocusID or gene name search: The user may enter a LocusID such as At3g24650, or a text field (such as NAC). The results are listed in a Search Results table. If the user marks the box in the first column and then moves to the bottom of the list, either the nucleotide or protein sequence can be retrieved. The family name, gene name, and description are displayed. In addition, there are four Arabidopsis resources the user may use to retrieve additional information, (M) for MIPS (Munich Institute for Protein Sequences): the MATDB within the MIPS website contains all Arabidopsis sequences and annotation produced by the Arabidopsis Genome Initiative plus mitochondrial and chloroplast genomes. Sequences were consolidated from European sequencing projects, Cold Spring Harbor Lab, and Washington University. (S) for SALK: Utilizing the SIGnAL Arabidopsis Gene Mapping Tool, it provides a map of the genome area in which the locus is found. One the map, cDNA (full-length cloned copies of mRNA) and T-DNA (sites of insertion of Agrobacterium T-DNA in the Arabidopsis genome) information is displayed in relation to the LocusID entered. (A) for TAIR (The Arabidopsis Information Resource): A genomic data resource, collected from a wide variety of sources, with information about genes, markers, polymorphisms, maps, sequences, clones, DNA and seed stocks, gene families and proteins.

b) Browse Families: There are 50 families (includes one family under the orphan category) of TFs currently listed. The user may click on a link to one of the families and see the same Search Results table as the Specific Search containing all TFs from the specific family.

For details please read AtTFDB HELP

AtRegNet - Arabidopsis Regulatory Network

  1. Start typing a TF name, and choose from the auto-complete suggestions
  2. Click “Show Interactions” to visualize interactions involving the selected TF
  3. In the visualization, click a circle representing a TF to show additional information
    • A table listing related interactions will appear below the visualization
  4. Click “Load more interactions” to load more interactions involving the selected TF
  5. Hover over the help icon in the top-left for more information
AtRegNet Labels: Confirmed vs Unconfirmed

Based on the analysis of the published literature, we have defined two groups of direct targets: confirmed and unconfirmed. A confirmed direct target has been defined as a gene that responds to a given TF according to the following criteria. (1) The TF binds directly to the regulatory region of the target gene, as shown by electrophoretic mobility shift assay, yeast one-hybrid analysis, and/or ChIP; or (2) the TF directly regulates the target gene, based on use of transgenic plants expressing an inducible TF-GR fusion protein, and the effect of CHX on the DEX activated/repressed genes; and (3) in vivo evidence of regulation showing expression of the target gene is affected by either loss-of-function mutations in the TF or ectopic expression of that TF in the plant.

An unconfirmed direct target is one that has been suggested to be a direct target of a given TF by one of the approaches described above.