AGRIS: Arabidopsis Gene Regulatory Information Server, an information resource of Arabidopsis cis-regulatory elements and transcription factors

By Ramana V. Davuluri, Hao Sun, Saranyan K. Palaniswamy, N. Matthews, Carlos Molina, M. Kurtz, Erich Grotewold. BMC Bioinformatics, 2003

420 citations recorded by the source corpus.

BackgroundThe gene regulatory information is hardwired in the promoter regions formed by cis-regulatory elements that bind specific transcription factors (TFs). Hence, establishing the architecture of plant promoters is fundamental to understanding gene expression. The determination of the regulatory circuits controlled by each TF and the identification of the cis-regulatory sequences for all genes have been identified as two of the goals of the Multinational Coordinated Arabidopsis thaliana Functional Genomics Project by the Multinational Arabidopsis Steering Committee (June 2002).ResultsAGRIS is an information resource of Arabidopsis promoter sequences, transcription factors and their target genes. AGRIS currently contains two databases, AtTFDB (Arabidopsis thaliana transcription factor database) and AtcisDB (Arabidopsis thaliana cis-regulatory database). AtTFDB contains information on approximately 1,400 transcription factors identified through motif searches and grouped into 34 families. AtTFDB links the sequence of the transcription factors with available mutants and, when known, with the possible genes they may regulate. Atcis DB consists of the 5' regulatory sequences of all 29,388 annotated genes with a description of the corresponding cis-regulatory elements. Users can search the databases for (i) promoter sequences, (ii) a transcription factor, (iii) a direct target genes for a specific transcription factor, or (vi) a regulatory network that consists of transcription factors and their target genes.ConclusionAGRIS provides the necessary software tools on Arabidopsis transcription factors and their putative binding sites on all genes to initiate the identification of transcriptional regulatory networks in the model dicotyledoneous plant Arabidopsis thaliana. AGRIS can be accessed from http://arabidopsis.med.ohio-state.edu.

Subfields: Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/680a793fefa138ddb6c4086b3a5e1c5a525697e2

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Citations in the corpus

Leaf Responses to Mild Drought Stress in Natural Variants of Arabidopsis1[OPEN] (2015, positive): “This analysis used the con ﬁ rmed regulatory interactions from the AGRIS (Davuluri et al., 2003; Palaniswamy al., 2006; Yilmaz et al., 2011) and microarray gene-target relations databases.”
Genome-Wide Reprogramming of Primary and Secondary Metabolism, Protein Synthesis, Cellular Growth Processes, and the Regulatory Infrastructure of Arabidopsis in Response to Nitrogen1[w] (2004, background): “….2,000 transcription factors or transcriptional regulators (Riechmann, 2002; http://www.arabidopsis.org; http://Arabidopsis.med.ohio-state.edu; Davuluri et al., 2003; http://genetics.mgh.harvard.edu/ sheenweb/AraTRs.html), and new classes of transcriptional regulators (TFs) are still being…”
The Botany Array Resource: e-Northerns, Expression Angling, and promoter analyses. (2005, neutral): “Links to PlantCARE (Rombauts et al. , 1999),PLACE (Higo et al. , 1999),AGRIS (Davuluri et al. , 2003) and Athena (http://wyrick.sbs.wsu.edu/Athena/; T .”
AGRIS: the Arabidopsis Gene Regulatory Information Server, an update (2010, background): “AtTFDB contains information on regulatory proteins, where TFs are grouped into families based on the presence of conserved domains and following prior classification criteria (7).”
Real-time RT-PCR profiling of over 1400 Arabidopsis transcription factors: unprecedented sensitivity reveals novel root- and shoot-specific genes. (2004, background): “RT-PCR profiling of Arabidopsis TFs 367 conditions (see Supplementary Material, Table S1).”
Evolutionary and comparative analysis of MYB and bHLH plant transcription factors. (2011, background): “…review, together withthe fully expanded names and other names that can be found in the literature or in AGRIS (http://arabidopsis.med.ohiostate.edu) (Davuluri et al., 2003) Abbreviated name Expanded and additional names AIB ABA-INDUCIBLE BHLH, AtbHLH017 ALC ALCATRAZ, AtbHLH073 AmCYC CYCLOIDEA…”
PlnTFDB: an integrative plant transcription factor database (2007, background): “Additionally, other TF databases focusing on single plant species are available (for A. thaliana [5-7], or O. sativa [8]).”