POBO

POBO summarizes, verifies, and screens predetermined cis-element motifs within promoter and upstream sequences to identify significantly over- and underrepresented transcription factor binding sites for analysis of gene regulation.

Key Features:

• Promoter bootstrapping: Detects and compares predefined transcription factor binding site motifs in promoters of co-regulated genes and calculates motif frequencies.
• Bootstrap analysis: Employs bootstrap analysis to identify motifs that are significantly over- or underrepresented in input promoter sets.
• Statistical tests: Incorporates statistical tests to increase true positive reliability and reduce false positives from pattern-discovery outputs.
• Hypothetical motif modification: Suggests slightly modified hypothetical motifs to aid distinguishing motifs associated with up- versus downregulated gene clusters.
• Pattern discovery: Facilitates discovery and verification of over-represented nucleotide patterns in upstream sequences to assess potential co-regulation by common cis-elements.

Scientific Applications:

• Gene expression data analysis: Applied to WRKY70 transgenic microarray data to show enrichment of WRKY-recognized motifs in both upregulated and downregulated clusters of plant defense pathways.
• Pathogen response studies: Used with pathogen-treated Arabidopsis thaliana to detect activated gene sets and suggest candidate transcription factors involved in immune responses.

Methodology:

Detects predetermined motifs in promoter regions of co-regulated genes, calculates motif frequencies, and tests significance using bootstrap analysis; it also supports discovery and verification of over-represented nucleotide patterns in upstream sequences.