ATCOECIS

ATCOECIS identifies coexpressed genes and associates coexpression neighborhoods with cis-regulatory motifs and Gene Ontology categories using high-throughput microarray transcript profiling data to predict gene function and regulatory modules in Arabidopsis thaliana.

Key Features:

• Gene Coexpression Analysis: Evaluates coexpression patterns and defines coexpression neighborhoods using the principle of guilt-by-association on microarray expression profiles.
• Integration with Gene Ontology (GO): Assesses GO enrichment within coexpression neighborhoods to support gene function prediction, reporting sensitivity scores of 13%–34%.
• Cis-Regulatory Element Enrichment: Detects enrichment of cis-regulatory motifs in coexpression neighborhoods, with 46% of neighborhoods reported as enriched for one or more motifs.
• Evolutionarily Conserved Motifs: Incorporates a curated set of evolutionarily conserved plant motifs to link motifs and genes to specific biological functions.
• OBP1 Case Study: Analysis of OBP1 transcriptome data revealed coexpressed modules associated with specific cis-regulatory elements and suggested a feed-forward regulatory interaction between OBP1 and the E2F pathway.
• User-Defined Gene Set Motif Analysis: Performs motif enrichment analysis on submitted gene sets to associate motifs with user-provided gene lists.

Scientific Applications:

• Predicting Gene Function: Infers functions for uncharacterized genes by combining coexpression, GO enrichment, and motif enrichment evidence.
• Identifying Regulatory Networks: Identifies candidate regulatory interactions and modules by linking coexpression neighborhoods with enriched cis-regulatory motifs.
• Discovering Cis-Regulatory Motifs: Facilitates discovery and functional association of novel or conserved cis-regulatory motifs with biological processes in Arabidopsis thaliana.

Methodology:

Uses high-throughput microarray transcript profiling data, applies guilt-by-association to define coexpression neighborhoods, assesses GO enrichment, tests cis-regulatory motif enrichment using a set of evolutionarily conserved plant motifs, and performs motif analysis on user-defined gene sets.