AGRIS: the Arabidopsis Gene Regulatory Information Server, an update

By Alper Yilmaz, M. K. Mejía-Guerra, K. Kurz, X. Liang, L. Welch, Erich Grotewold. Nucleic Acids Res., 2010

349 citations recorded by the source corpus.

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.

Subfields: Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/ef46c8c6c7266e8d8c821e1f4e26d087a9a7ed1f

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In Molecular Biology

1. Xinbin Dai
2. Patrick Xuechun Zhao
3. Peifen Zhang
4. G. Martin
5. Ge Gao
6. Seung Yon Rhee
7. Lei Kong
8. Lieven Clement

In Plant Science

1. Xinbin Dai
2. Patrick Xuechun Zhao
3. G. Martin
4. Ge Gao
5. James J. Giovannoni

Citations in the corpus

• PlantTFDB 3.0: a portal for the functional and evolutionary study of plant transcription factors (2013, background): “In the following years, several databases dedicated to identification and annotation of plant TFs became publicly available, either for multiple species, such as PlnTFDB (2), PlanTAPDB (3), GRASSIUS (4), LegumeTFDB (5), DATFAP (6) and TreeTFDB (7), or for individual organisms, such as AGRIS (8), RAR”
• PlantPAN 2.0: an update of plant promoter analysis navigator for reconstructing transcriptional regulatory networks in plants (2015, background): “Among them, AGRIS is dedicated to amassing information on transcriptional regulation (e.g. TFs, cis-regulatory elements and experimentally validated gene regulatory networks) in Arabidopsis , containing three sub-databases, At cis DB, AtTFDB and AtRegNet (8).”
• iTAK: A Program for Genome-wide Prediction and Classification of Plant Transcription Factors, Transcriptional Regulators, and Protein Kinases. (2016, methodology): “The families in PlantTFcat (Dai et al., 2013) and AtTFDB (Yilmaz et al., 2011) were used as supporting evidence, as they use different methods for domain identification, therefore cannot be directly compared with PlnTFDB and PlantTFDB.”
• 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.”