AGRIS and AtRegNet. A Platform to Link cis-Regulatory Elements and Transcription Factors into Regulatory Networks

Abstract

Gene regulatory pathways converge at the level of transcription, where interactions among regulatory genes and between regulators and target genes result in the establishment of spatiotemporal patterns of gene expression. The growing identification of direct target genes for key transcription factors (TFs) through traditional and high-throughput experimental approaches has facilitated the elucidation of regulatory networks at the genome level. To integrate this information into a Web-based knowledgebase, we have developed the Arabidopsis Gene Regulatory Information Server (AGRIS). AGRIS, which contains all Arabidopsis (Arabidopsis thaliana) promoter sequences, TFs, and their target genes and functions, provides the scientific community with a platform to establish regulatory networks. AGRIS currently houses three linked databases: AtcisDB (Arabidopsis thaliana cis-regulatory database), AtTFDB (Arabidopsis thaliana transcription factor database), and AtRegNet (Arabidopsis thaliana regulatory network). AtTFDB contains 1,690 Arabidopsis TFs and their sequences (protein and DNA) grouped into 50 (October 2005) families with information on available mutants in the corresponding genes. AtcisDB consists of 25,806 (September 2005) promoter sequences of annotated Arabidopsis genes with a description of putative cis-regulatory elements. AtRegNet links, in direct interactions, several hundred genes with the TFs that control their expression. The current release of AtRegNet contains a total of 187 (September 2005) direct targets for 66 TFs. AGRIS can be accessed at http://Arabidopsis.med.ohio-state.edu.

Systematic Identification of Functional Plant Modules through the Integration of Complementary Data Sources

“…The PPI data were downloaded from the CORNET database in November 2010 (De Bodt et al, 2010), and only experimentally identified PPIs were retained. Interaction data of TFs and their targets were retrieved from the AtRegNet database in November 2010 (Palaniswamy et al, 2006). The targets of each TF were divided based on the effect on their expression: activation, repression, and all (this group also contains the genes with unknown effect).…”

“…MotifSampler and Weeder exclusively supported 1,190 (77.1%) and 285 (18.5%) motifs, respectively, while 69 (4.5%) motifs were supported by both tools, emphasizing their complementarity. To validate the reliability of motifs found by only one tool, the overlap of motifs found by MotifSampler or Weeder was compared with a set of 515 known motifs from PLACE (Higo et al, 1999) and AGRIS (Palaniswamy et al, 2006). Of the 1,544 de novo motif instances in modules, 528 corresponded to a known motif.…”

“…Based on an ensemble of primary data sets covering TF target interactions from AtRegNet (Palaniswamy et al, 2006), probabilistic gene-gene associations from AraNet (Lee et al, 2010), nonelectronic gene-GO annotations from The Arabidopsis Information Resource (TAIR; Berardini et al, 2004), and PPIs from CORNET (De Bodt et al, 2010), functional gene modules were delineated in Arabidopsis (Table I). To assemble a set of high-quality gene associations, the GO, PPI, and TF target data were filtered to only contain experimental information (see "Materials and Methods").…”

“…Based on these results, a set of nonredundant motifs was defined for each module, and motifs with a similar sequence but residing in a distinct set of genes, were considered as distinct motifs. Known motifs were extracted from AGRIS (Palaniswamy et al, 2006) and PLACE (Higo et al, 1999), and the redundancy was removed similarly as for the modules.…”

Comparative Network Analysis Reveals That Tissue Specificity and Gene Function Are Important Factors Influencing the Mode of Expression Evolution in Arabidopsis and Rice

“…First, known plant DNA motifs from AGRIS (Palaniswamy et al, 2006) and PLACE (Higo et al, 1999) were mapped onto the 1-kb upstream promoters followed by motif enrichment analysis per gene-centric cluster . To reduce the inclusion of false-positive motif instances, for a given gene-centric cluster, only motifs present in the seed gene promoter and significantly enriched in the corresponding coexpression cluster were retained for further analysis.…”