RESOURCESRESOURCES

Transcriptional Elements

Tools and resources for the analysis, characterization and comparison of sequence elements that influence transcription in Arabidopsis and other plants.

AGRIS- The Arabidopsis Gene Regulatory Information Server

http://arabidopsis.med.ohio-state.edu/

Arabidopsis Gene Regulatory Information Server. An information resource of Arabidopsis cis regulatory elements and transcription factors.

From the abstract: 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. Tools recently incorporated into AGRIS include 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.

Araboxcis

http://araboxcis.org/

Arabidopsis has undergone massive expansion of TF families, and many members of the same family are capable of binding to the same motifs (conserved cis-regulatory boxes). This makes it difficult to identify which TF influences which downstream genes.

This website allows you to look through and download data related to how bHLHs and bZIPs (which are expressed in seedlings) regulate genes downstream of perfect G-boxes (CACGTG).

Database of Arabidopsis Transcription Factors (DATF)

http://datf.cbi.pku.edu.cn/

The Database of Arabidopsis Transcription Factors (DATF) collects all Arabidopsis transcription factors (total 1922 Loci; 2290 Gene Models) and classifies them into 64 families.

From the abstract: The DATF contains known and predicted Arabidopsis transcription factors (1827 genes in 56 families) with the unique information of 1177 cloned sequences and many other features including 3D structure templates, EST expression information, transcription factor binding sites and nuclear location signals.

EARS

http://wsbc.warwick.ac.uk/ears/

Comparative genomics tool used to search for alignment conserved regions in orthologous regulatory regions from plants.

From the abstract: Here, we demonstrate a robust and highly sensitive, in silico method to identify evolutionarily conserved regions within non-coding DNA. Sequence conservation within these regions is taken as evidence for evolutionary pressure against mutations, which is suggestive of functional importance.

ePLANT

https://www.araport.org/eplant

ePlant is a visual analytic tool created by the Bio-Analytic Resource for Plant Biology at the University of Toronto for exploring multiple levels of Arabidopsis data through a zoomable user interface. ePlant connects to several publicly available web services to download genome, proteome, interactome, transcriptome, and 3D molecular structure data for one or more genes or gene products of interest. Data are displayed with a set of visualization tools that are presented using a conceptual hierarchy from big to small, and many of the tools combine information from more than one data type.

Expresso

https://bioinformatics.cs.vt.edu/expresso/

Expresso is a web server designed to identify and explore the binding of transcription factors to their target genes in plants using available ChIP-Seq data.

Services available:

> Search for a transcription factor and identify its target genes in the Expresso database

> Search for selected target genes and identify their candidate transcription factors based on available ChIP-Seq data:

> Upload your own gene expression data in order to identify highly correlating pairs of transcription factors and inferred targets genes

 

Plant cis-Acting Regulatory Elements (Plant CARE)

http://bioinformatics.psb.ugent.be/webtools/plantcare/html/

A referential database with 435 different names of plant transcription sites describing more than 159 plant promoters and the possibility to store all plant transcription sites, consensus and matrices described in the literature into the database. Use Plant CARE to run sophisticated queries on the data, like looking for sites linked to a specific function, and submit a sequence to a program which will look for transcription sites known by PlantCARE.

From the abstract: PlantCARE is a database of plant cis-acting regulatory elements, enhancers and repressors. Regulatory elements are represented by positional matrices, consensus sequences and individual sites on particular promoter sequences. Data about the transcription sites are extracted mainly from the literature, supplemented with an increasing number of in silico predicted data. 

PlantNATsDB

http://bis.zju.edu.cn/pnatdb/?species=ath

A comprehensive database of plant natural antisense transcripts, a type of regulatory RNA. It has a user-friendly interface, including a simple 'viewer' as well as a search option. 

From the abstract: PlantNATsDB is currently the most comprehensive resource of NATs in the plant kingdom, which can serve as a reference database to investigate the regulatory function of NATs. The PlantNATsDB is freely available at http://bis.zju.edu.cn/pnatdb/

PlantProm DB

http://linux1.softberry.com/berry.phtml?topic=plantprom&group=data&subgroup=plantprom

The new release of PlantProm DB contains 578 unrelated entries including 151, 396 and 31 promoters with experimentally verified TSS from monocot, dicot and other plants, respectively.

From the abstract: PlantProm DB, a plant promoter database, is an annotated, non-redundant collection of proximal promoter sequences for RNA polymerase II with experimentally determined transcription start site(s), TSS, from various plant species.

plantpromoterDB

http://ppdb.agr.gifu-u.ac.jp/ppdb/cgi-bin/index.cgi

A plant promoter database that provides promoter annotation of Arabidopsis and rice. Contains information on promoter structures, transcription start sites (TSSs) that have been identified from full-length cDNA clones and also a vast amount of TSS tag data.