TilingScan

TilingScan identifies and visualizes differentially expressed DNA regions across entire genomes using tiling microarray and next-generation sequencing data for genome-wide transcriptional analysis.

Key Features:

• Genome-wide detection: Identifies differentially expressed regions across entire genomes from tiling microarray and next-generation sequencing data.
• Strand-specific analysis: Performs strand-specific detection of expressed RNA sequences.
• Non-coding RNA and novel transcript discovery: Detects transcriptional variation in non-coding RNAs and unannotated genomic regions.
• Comparative analysis: Compares experimental conditions to locate regions with differential expression between states.
• Reference-genome integration: Analyzes datasets in conjunction with all known features of a given reference genome.
• Custom region detection: Enables detection of differentially expressed regions without restricting analysis to annotated protein-coding genes.

Scientific Applications:

• Genome-wide transcriptional profiling: Profiling transcriptional activity across genomes using tiling microarray and next-generation sequencing data.
• Novel transcript and regulatory element discovery: Identification of novel transcripts and potential regulatory elements, including non-coding RNAs.
• Comparative transcriptomics: Detecting transcriptional changes between experimental conditions to study gene regulation and cellular responses.
• Unannotated locus characterization: Characterizing differential expression in unpredicted or unannotated genomic regions.

Methodology:

Analyzes tiling microarray and next-generation sequencing data with strand-specific detection and visualization of differentially expressed genomic regions; implemented using PHP and JavaScript.