BEARR

BEARR performs batch extraction and analysis of cis-regulatory regions to identify transcription factor binding sites from gene lists derived from microarray data.

Key Features:

• Gene Identifier Input: Accepts lists of gene identifiers such as RefSeq and Unigene IDs derived from microarray data.
• Pattern Matching Capabilities: Allows input of consensus patterns and optionally a position weight matrix and identifies matches on both sense and anti-sense strands of genomic sequences.
• Regulatory Region Analysis: Enables specification of search distances upstream and downstream relative to transcription start sites and 3' termini to locate potential regulatory elements.
• Batch Extraction and Microarray Integration: Integrates with microarray outputs to perform batch extraction and analysis of cis-regulatory regions from large gene sets.

Scientific Applications:

• Transcription Factor Target Identification: Pinpoints specific binding sites in cis-regulatory regions of differentially expressed genes to identify direct transcription factor targets.
• Regulatory Network Modeling: Provides binding-site data usable for construction and analysis of transcriptional regulatory networks.
• Experimental and Clinical Target Mining: Generates candidate regulatory targets for experimental manipulation or clinical investigation.

Methodology:

Accepts gene identifier lists (e.g., RefSeq, Unigene) from microarray outputs, performs pattern matching using consensus patterns or an optional position weight matrix on both sense and anti-sense strands, and searches specified upstream/downstream windows relative to transcription start sites and 3' termini to extract and analyze cis-regulatory regions.