AtREA - Arabidopsis thaliana regulatory element analyzer

AtREA is a collection of  programs for analysis of  distribution, features and combination of known and novel CREs (Cis-Regulatory Elements ) in Arabidopsis functional classes, metabolic pathways, genome wide microarray and user defined datasets.

Distribution of CRE:
The CRE distribution analysis module in ATREA has been designed to study CRE distribution in arabidopsis functional classes and coexpressed gene sets. The functional classes that can be analyzed using this module includes all three Gene Ontology(GO) categories -biological process(GOBP), molecular function(GOMF) and cellular component(GOCC) and MIPS FUNCAT subgroups. This module can be also used to metabolic pathways and expression classes (derived from microarray data). Many known Arabidopsis CREs require the presence of a second CRE in nearby region to be functional (ABRE, for example,requires the presence of a coupling element(CE) ) and therefore occur as structured cis-regulatory pairs or modules. The CRE pairs subsection can be used to study the distribution of such CRE pairs where both the component CREs as well as maximum and minimum distance within them can be specified in the input menu. The CRE-combination subsection can receive a set of up to four different CREs (separated by hash sign) as input and analyze their distribution in functional and expression classes.

CRE feature analysis module

Evaluation of CRE features:
CRE feature analysis module of AtREA can be used to evaluate strand and positional trends in a CREs distribution in upstream sequences in Arabidopsis genome. Moreover by selecting an expression slide and expression type from slide and expression type menu, this analysis can be applied to a specific expression dataset/user deifned list fo genes, which in addition of detecting strand and positional preference also evaluates the impact of position and strand in expression. For many CREs like ACGT core consensus it has been shown that the frequency of occurrence of this CRE in promoter can have direct impact on expression. The "frequency" option from the CRE feature menu can be used to analyze the impact of multiple occurrences of a CRE in expression of genes. The “variant” analysis option generates all possible single nucleotide variants of the supplied CRE and compares the distribution of these variants with the original user defined CRE both in genome and the selected expression dataset.

Promoter state analysis module

Promoter state analysis tool:
The promoter state module of AtREA has been designed to study the role of CREs/CRE combinations in regulation of gene expression. This module takes as input a set of induced/repressed genes(from expression dataset/or user defined list) and a set of CREs that may be involved in expression regulation under the given condition, which can be derived from literature/experimental data and/or computational analysis. The module first segregates the upstream sequence set into CRE states based on presence/frequency of occurrence of each of the user defined CREs. The module then compares the expected frequency of occurrence of each of the states (assumed from their respective genomic occurrences) to their actual frequency of occurrence in the selected gene set and identify overrepresented states in the selected gene set. The CRE state module can therefore be applied for identification of CRE/CRE combinations that show significant over representation in induced/repressed genes in a experimental condition and also to recognize CRE combination which show significant difference in expression compared to expression of the component CREs.

Future Improvements

In the next version of AtREA we plan to include:

A module for CRE conservation analysis among different plant species.
Increase the upstream sequence length and inlcude UTRs in the sequence dataset

To cite AtREA please refer to:
Choudhury A and Lahiri A (2008) Arabidopsis thaliana regulatory element analyzer Bioinformatics, 24: 2263 - 2264.
Department of Biophysics, Molecular Biology and Genetics,
University of Calcutta, India

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