CONFAC

CONFAC identifies conserved transcription factor binding sites (TFBSs) in non-coding regulatory regions between human and mouse and integrates DNA microarray and vertebrate genome sequencing data for comparative analysis of gene regulation.

Key Features:

• Comparative Genomic Analysis: Compares non-coding regulatory sequences between human and mouse genomes to identify conserved TFBSs.
• High-Throughput Capability: Processes hundreds of genes simultaneously for large-scale genomic studies.
• Enrichment Analysis: Identifies TFBSs significantly enriched in promoter regions of gene clusters derived from microarray analyses by comparing to control gene sets using the Mann-Whitney U-test.
• Low False Positive Rate: Validated to maintain over 98% of TFBSs with false positive rates below 5%.
• Data Integration: Integrates DNA microarray data with vertebrate genome sequencing information to inform TFBS detection.
• Orthologue-Based Input: Uses lists of human gene names and identifiers and compares them with corresponding mouse orthologues.

Scientific Applications:

• Comparative gene regulation analysis: Elucidates transcriptional control mechanisms conserved between humans and mice by identifying functionally important TFBSs.
• Validation of TFBSs: Confirms experimentally established regulatory elements, as demonstrated across multiple microarray studies.

Methodology:

Accepts input lists of human gene names and identifiers and compares them with mouse orthologues; analyzes non-coding regulatory sequences between species to pinpoint conserved TFBSs; employs the Mann-Whitney U-test to assess TFBS enrichment in gene cluster promoters versus control sets; includes validation studies demonstrating the reported accuracy.