AGRIS: the Arabidopsis Gene Regulatory Information Server, an update

Abstract

The Arabidopsis Gene Regulatory Information Server (AGRIS; http://arabidopsis.med.ohio-state.edu/) provides a comprehensive resource for gene regulatory studies in the model plant Arabidopsis thaliana. Three interlinked databases, AtTFDB, AtcisDB and AtRegNet, furnish comprehensive and updated information on transcription factors (TFs), predicted and experimentally verified cis-regulatory elements (CREs) and their interactions, respectively. In addition to significant contributions in the identification of the entire set of TF-DNA interactions, which are the key to understand the gene regulatory networks that govern Arabidopsis gene expression, tools recently incorporated into AGRIS include the complete set of words length 5-15 present in the Arabidopsis genome and the integration of AtRegNet with visualization tools, such as the recently developed ReIN application. All the information in AGRIS is publicly available and downloadable upon registration.

Figure 1.

AtTFDB query result table. Either TF family browsing or search query results indicate Locus ID, synonyms, links, sequences and AtRegNet related data. The updated AtTFDB provides improved integration with AtRegNet. Confirmed direct target counts are indicated with ‘C’, and unconfirmed one are indicated with ‘U’.

Figure 2.

Results of querying word frequencies. Occurrence, scoring and positional distribution of a given word is calculated for various genomic segments. (A) A query is initiated by entering a word 5–15 letters (e.g. CTAACCA) in length into the search box. (B) The user is notified if the queried word matches a known CRE available in AtcisDB. (C) Total occurrences include possible multiple occurrences within a single sequence. For instance, CTAACCA is found a total of 138 times in 5′-UTR region sequences, and 135 genes contain this word in their 5′-UTR regions. Expected occurrences are calculated by a Hidden Markov Model, as described in ref. 14. The unique sequence occurrences column is hyperlinked to a list of genes that contain the word in the corresponding segments. (D) Flot (http://code.google.com/p/flot/), a Javascript plotting library, was used for visualization of positional distribution of a word within different sets. Only Proximal and Distal Promoters segments are shown here. Charts are interactive and are capable of zooming into a desired region.

Figure 3.

Screenshot from AGRIS depicting features of ReIN. For each Locus ID or gene name available in the AtRegNet database, ReIN displays all interactions involving the searched gene. Detailed descriptions of features are available in REIN tutorial page (http://arabidopsis.med.ohio-state.edu/REIN/ReINtutorial.html).