The Arabidopsis Information Resource (TAIR): a model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community

Rhee, Seung Y.; Beavis, William D.; Berardini, Tanya Z.; Chen, Guang-Hong; Dixon, David A.; Doyle, Aisling; Garcia-Hernández, M.; Huala, Eva; Lander, Gabriel C.; Montoya, Mary; Miller, Neil; Mueller, Lukas A.; Mundodi, Suparna; Reiser, Leonore; Tacklind, Julie; Weems, Dan C.; Wu, Yihe; Xu, Iris; Yoo, Daniel; Yoon, Jungwon; Zhang, Peifen

doi:10.1093/nar/gkg076

Cited by 784 publications

(594 citation statements)

References 8 publications

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“…We use the 63 TSS locations identified in Xie et al (2005) to prepare a set of miRNA upstream promoter regions as follows: we compute the genomic location of the TSS associated with each miRNA, and identify the nearest upstream gene for each miRNA TSS using the TAIR6 genome annotation release (Rhee et al 2003). In cases in which multiple TSSs were identified upstream of a single miRNA, we restricted ourselves to the downstream-most TSS so that we were considering the largest possible promoter region.…”

Section: Promoter Sequence Selectionmentioning

confidence: 99%

MicroRNA promoter element discovery in Arabidopsis

Megraw

Baev²,

Rusinov³

et al. 2006

RNA

168

138

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In this study we present a method of identifying Arabidopsis miRNA promoter elements using known transcription factor binding motifs. We provide a comparative analysis of the representation of these elements in miRNA promoters, protein-coding gene promoters, and random genomic sequences. We report five transcription factor (TF) binding motifs that show evidence of overrepresentation in miRNA promoter regions relative to the promoter regions of protein-coding genes. This investigation is based on the analysis of 800-nucleotide regions upstream of 63 experimentally verified Transcription Start Sites (TSS) for miRNA primary transcripts in Arabidopsis. While the TATA-box binding motif was also previously reported by Xie and colleagues, the transcription factors AtMYC2, ARF, SORLREP3, and LFY are identified for the first time as overrepresented binding motifs in miRNA promoters.

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Section: Promoter Sequence Selectionmentioning

confidence: 99%

MicroRNA promoter element discovery in Arabidopsis

Megraw

Baev²,

Rusinov³

et al. 2006

RNA

168

138

View full text Add to dashboard Cite

show abstract

“…29 GOSlim annotation developed by TAIR was used to organize sets of genes into broad ontology categories. 30 transcription, [17][18][19][20] pre-mRNA splicing, 21 and RNA silencing. 22,23 Arabidopsis genome has 2 partly redundant TSN genes (TSN1 and TSN2) which were shown to confer stress tolerance through the stabilization of mRNAs encoding secreted proteins 24 and gibberellin 20-oxidase 3, a key enzyme in gibberellin biosynthesis.…”

mentioning

confidence: 99%

Tudor Staphylococcal Nuclease plays two antagonistic roles in RNA metabolism under stress

Gutiérrez-Beltrán

Bozhkov

Moschou

2015

Plant Signaling & Behavior

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“…[26,27]). Among these, we here consider AtCOECiS [28], ATTED II [29], BAR [30], CoP [31], CORNET [32], Cress Express [33], CSB.DB [34], GeneCAT [35], GeneMania [36], Genevestigator [37], PlaNet [38].…”

Section: Introductionmentioning

confidence: 99%

Gene co-expression analyses: an overview from microarray collections inArabidopsis thaliana

et al. 2016

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Bioinformatics web-based resources and databases are precious references for most biological laboratories worldwide. However, the quality and reliability of the information they provide depends on them being used in an appropriate way that takes into account their specific features. Huge collections of gene expression data are currently publicly available, ready to support the understanding of gene and genome functionalities. In this context, tools and resources for gene co-expression analyses have flourished to exploit the 'guilty by association' principle, which assumes that genes with correlated expression profiles are functionally related. In the case of Arabidopsis thaliana, the reference species in plant biology, the resources available mainly consist of microarray results. After a general overview of such resources, we tested and compared the results they offer for gene co-expression analysis. We also discuss the effect on the results when using different data sets, as well as different data normalization approaches and parameter settings, which often consider different metrics for establishing co-expression. A dedicated example analysis of different gene pools, implemented by including/excluding mutant samples in a reference data set, showed significant variation of gene co-expression occurrence, magnitude and direction. We conclude that, as the heterogeneity of the resources and methods may produce different results for the same query genes, the exploration of more than one of the available resources is strongly recommended. The aim of this article is to show how best to integrate data sources and/or merge outputs to achieve robust analyses and reliable interpretations, thereby making use of diverse data resources an opportunity for added value.

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The Arabidopsis Information Resource (TAIR): a model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community

Cited by 784 publications

References 8 publications

MicroRNA promoter element discovery in Arabidopsis

MicroRNA promoter element discovery in Arabidopsis

Tudor Staphylococcal Nuclease plays two antagonistic roles in RNA metabolism under stress

Gene co-expression analyses: an overview from microarray collections inArabidopsis thaliana

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